Volcanos
Before running this script, you need to run all the analysis first so the variable are available.
run volcanos for all the comparisons of interest
Get comparisons
ls(all.names = TRUE) [1] ".Random.seed" "adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic" "agbmi_df"
[4] "base_path" "bone_hip_vs_tibia" "bone_non_sclerotic_hip_vs_tibia"
[7] "bone_sclerotic_hip_vs_tibia" "c" "col_sums"
[10] "color_palette" "column_to_plot" "common_genes"
[13] "comparison_names" "comparisons_list" "df"
[16] "hip_adipocytes_sclerotic_vs_non_sclerotic" "hip_pellet_sclerotic_vs_non_sclerotic" "hip_sclerotic_vs_non_sclerotic"
[19] "m_pca_hip" "m_pca_hip_t" "m_pca_hip_transposed_adipocytes"
[22] "m_pca_hip_transposed_pellet" "m_pca_samples_bone" "m_pca_tibia"
[25] "m_pca_tibia_t" "m_pca_tibia_transposed_adipocytes" "m_pca_tibia_transposed_pellet"
[28] "m_samples_bone" "matrix_counts_hip" "matrix_counts_tibia"
[31] "md" "md_df" "md_df_bone"
[34] "md_df_hip" "md_df_split" "md_df_tibia"
[37] "mean_sum" "normalize_and_pca" "p"
[40] "path" "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic" "percentiles"
[43] "percentVar_obj" "plot_the_pca" "plot_volcano"
[46] "pp" "quantiles" "results"
[49] "run_pca_structuring" "run_pca_structuring_2" "save_results_deg"
[52] "sums_mm" "sums_mm_hip" "sums_mm_tibia"
[55] "test_diff_exp" "tibia_adipocytes_sclerotic_vs_non_sclerotic" "tibia_pellet_sclerotic_vs_non_sclerotic"
[58] "tibia_sclerotic_vs_non_sclerotic" "time_taken" "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"
[61] "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic" "volcano_hip_adipocytes_sclerotic_vs_non_sclerotic" "volcano_hip_pellet_sclerotic_vs_non_sclerotic"
[64] "volcano_hip_sclerotic_vs_non_sclerotic" "volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic" "volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic"
[67] "volcano_tibia_pellet_sclerotic_vs_non_sclerotic" "volcano_tibia_sclerotic_vs_non_sclerotic" "y"
[70] "y_norm" "y_normalized_corrected" "y_normalized_corrected_pcas"
[73] "y_normalized_corrected_pcas_df" # Get all object names that match a pattern
comparison_names <- ls(pattern = "vs")
comparison_names [1] "adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic" "bone_hip_vs_tibia" "bone_non_sclerotic_hip_vs_tibia"
[4] "bone_sclerotic_hip_vs_tibia" "hip_adipocytes_sclerotic_vs_non_sclerotic" "hip_pellet_sclerotic_vs_non_sclerotic"
[7] "hip_sclerotic_vs_non_sclerotic" "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic" "tibia_adipocytes_sclerotic_vs_non_sclerotic"
[10] "tibia_pellet_sclerotic_vs_non_sclerotic" "tibia_sclerotic_vs_non_sclerotic" "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"
[13] "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic" "volcano_hip_adipocytes_sclerotic_vs_non_sclerotic" "volcano_hip_pellet_sclerotic_vs_non_sclerotic"
[16] "volcano_hip_sclerotic_vs_non_sclerotic" "volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic" "volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic"
[19] "volcano_tibia_pellet_sclerotic_vs_non_sclerotic" "volcano_tibia_sclerotic_vs_non_sclerotic" comparisons_list <- mget(comparison_names)
comparisons_list$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$results
Coefficient: groupsclerotic
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$colsums_samples
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$normalized_matrix
X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte
TSPAN6 6.204800e+00 4.542855e+00 1.862113e+01 4.562555e+00 9.878102e+00
TNMD 0.000000e+00 0.000000e+00 7.161971e+00 1.520852e+00 9.188932e-01
DPM1 9.996622e+00 1.249285e+01 4.297183e+00 9.632061e+00 1.608063e+01
SCYL3 8.962489e+00 9.842853e+00 1.002676e+01 3.041703e+00 2.297233e+00
C1orf112 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.297233e-01
FGR 3.998649e+01 1.377999e+02 2.291831e+01 6.641052e+01 3.928268e+01
CFH 1.378844e+00 4.164284e+00 1.432394e+00 6.590357e+00 4.135019e+00
FUCA2 2.688747e+01 1.249285e+01 4.297183e+00 1.318071e+01 1.171589e+01
GCLC 2.619804e+01 2.763570e+01 6.087676e+01 9.125110e+00 3.308015e+01
NFYA 1.792498e+01 5.337855e+01 3.437746e+01 5.322981e+01 2.021565e+01
STPG1 1.103076e+01 3.785713e-01 7.161971e-01 5.576456e+00 2.756680e+00
NIPAL3 8.962489e+00 4.164284e+00 1.647253e+01 1.318071e+01 3.216126e+00
LAS1L 3.136871e+01 8.744996e+01 3.509366e+01 4.207690e+01 4.663383e+01
ENPP4 0.000000e+00 2.271428e+00 7.161971e-01 5.069506e-01 6.202529e+00
SEMA3F 4.136533e+01 8.744996e+01 4.941760e+01 3.345874e+01 1.516174e+01
ANKIB1 1.378844e+01 1.211428e+01 1.289155e+01 1.470157e+01 1.378340e+01
CYP51A1 1.689084e+01 6.814283e+00 5.013380e+00 1.165986e+01 8.729485e+00
X109_tibia_sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte
TSPAN6 1.021426e+01 7.349113e+00 4.873022e+00 7.805789e+00 3.095194
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000
DPM1 1.407299e+01 1.561687e+01 5.847626e+00 1.059357e+01 13.412508
SCYL3 2.950787e+00 1.837278e+00 4.873022e+00 2.230225e+00 0.000000
C1orf112 4.993640e+00 0.000000e+00 0.000000e+00 5.575564e-01 0.000000
FGR 8.284903e+01 3.858284e+01 3.411115e+01 2.255316e+02 206.346277
CFH 5.220624e+00 1.837278e+00 0.000000e+00 1.115113e+00 4.126926
FUCA2 1.770472e+01 2.066938e+01 1.656827e+01 1.115113e+01 12.380777
GCLC 3.563643e+01 2.755917e+01 3.800957e+01 3.735628e+01 26.825016
NFYA 1.838567e+01 1.699482e+01 5.652705e+01 2.732026e+01 17.539434
STPG1 6.355542e+00 1.837278e+00 2.923813e+00 6.969455e+00 0.000000
NIPAL3 8.171411e+00 1.286095e+01 8.771439e+00 1.784180e+01 4.126926
LAS1L 4.880148e+01 3.628625e+01 3.411115e+01 2.927171e+01 11.349045
ENPP4 1.815869e+00 2.296598e+00 3.898417e+00 1.449647e+01 4.126926
SEMA3F 2.564915e+01 2.066938e+01 2.144130e+01 4.209551e+01 15.475971
ANKIB1 9.987280e+00 1.469823e+01 3.313655e+01 1.226624e+01 16.507702
CYP51A1 1.725076e+01 2.296598e+01 1.266986e+01 8.084567e+00 3.095194
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte
TSPAN6 4.669196e+00 7.331045e+00 5.444540e+00 1.055755e+01 1.277559e+01
TNMD 7.183378e-02 0.000000e+00 4.949581e-01 0.000000e+00 2.814961e+00
DPM1 1.249908e+01 1.241548e+01 1.666359e+01 2.413154e+01 1.429134e+01
SCYL3 3.591689e+00 3.665522e+00 2.969749e+00 3.016443e+00 2.598426e+00
C1orf112 1.149341e+00 1.655397e+00 3.134735e+00 0.000000e+00 0.000000e+00
FGR 2.295089e+02 1.115028e+02 2.479740e+02 4.735816e+02 5.283466e+01
CFH 1.795845e+00 2.601338e+00 3.299721e-01 0.000000e+00 5.629923e+00
FUCA2 1.537243e+01 1.619924e+01 1.600365e+01 4.524665e+00 1.710630e+01
GCLC 4.662013e+01 3.027012e+01 7.341879e+01 1.266906e+02 3.464568e+01
NFYA 3.103219e+01 2.707757e+01 4.306136e+01 6.032886e+01 3.139765e+01
STPG1 7.470714e+00 1.891882e+00 9.074233e+00 9.049329e+00 5.196852e+00
NIPAL3 1.530060e+01 6.621589e+00 1.484874e+01 6.032886e+00 8.877955e+00
LAS1L 3.598873e+01 3.488158e+01 3.695687e+01 2.262332e+01 3.486222e+01
ENPP4 2.729684e+00 3.429037e+00 4.619609e+00 4.524665e+00 1.234252e+01
SEMA3F 2.521366e+01 1.454385e+01 4.817593e+01 1.809866e+01 2.750001e+01
ANKIB1 1.206808e+01 1.537155e+01 1.666359e+01 0.000000e+00 1.364174e+01
CYP51A1 9.697561e+00 1.135129e+01 1.468376e+01 1.508222e+00 1.147638e+01
X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte
TSPAN6 1.149548e+01 1.841704e+00 0.000000e+00 5.196115e+00 7.432058e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.405392e+00 1.197108e+01 2.775202e+01 1.160063e+01 1.300610e+01
SCYL3 7.315305e+00 5.064687e+00 0.000000e+00 2.537638e+00 4.645036e-01
C1orf112 6.966957e-01 0.000000e+00 0.000000e+00 3.625197e-01 0.000000e+00
FGR 5.329722e+01 3.315068e+01 1.591116e+02 5.691559e+01 5.388242e+01
CFH 4.528522e+00 5.525113e+00 9.250672e+00 2.175118e+00 6.038547e+00
FUCA2 1.602400e+01 2.900685e+01 1.480108e+01 1.389659e+01 2.647671e+01
GCLC 1.706904e+01 2.900685e+01 2.405175e+01 3.673533e+01 9.754576e+00
NFYA 3.692487e+01 1.519406e+01 0.000000e+00 2.271790e+01 2.926373e+01
STPG1 8.012000e+00 1.243151e+01 0.000000e+00 5.800315e+00 2.787022e+00
NIPAL3 1.254052e+01 5.064687e+00 1.850134e+01 1.172147e+01 7.432058e+00
LAS1L 2.717113e+01 3.683409e+01 1.850134e+01 4.495244e+01 4.691487e+01
ENPP4 4.876870e+00 1.657534e+01 0.000000e+00 7.008713e+00 6.503051e+00
SEMA3F 3.413809e+01 1.887747e+01 2.590188e+01 1.595087e+01 1.439961e+01
ANKIB1 1.428226e+01 2.117960e+01 1.480108e+01 1.945522e+01 7.896562e+00
CYP51A1 1.184383e+01 1.841704e+00 4.625336e+01 8.217112e+00 1.672213e+01
X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte X160_Tibia_non.sclerotic_adipocyte
TSPAN6 9.581084e+00 2.545339e+00 9.840294e+00 8.902905e+00 1.119467e+01
TNMD 1.532973e+00 0.000000e+00 1.192763e+00 1.440176e+00 9.950816e-01
DPM1 7.537119e+00 9.454116e+00 1.177853e+01 1.112863e+01 1.285314e+01
SCYL3 4.854416e+00 1.818099e+00 5.367433e+00 3.927752e-01 2.238934e+00
C1orf112 1.277478e+00 0.000000e+00 2.981907e-01 2.618502e-01 6.633877e-01
FGR 3.755785e+01 2.654425e+01 1.938240e+01 2.867259e+01 1.393114e+01
CFH 5.109912e-01 1.090860e+00 2.087335e+00 2.094801e+00 2.156010e+00
FUCA2 1.775694e+01 7.636017e+00 1.684778e+01 1.911506e+01 1.617008e+01
GCLC 3.232019e+01 2.690787e+01 3.339736e+01 4.268158e+01 3.681802e+01
NFYA 4.675569e+01 2.581701e+01 2.788083e+01 3.155294e+01 3.225723e+01
STPG1 9.581084e+00 1.454479e+00 3.727384e+00 5.891628e+00 8.126500e+00
NIPAL3 2.414433e+01 8.726876e+00 8.647531e+00 1.086678e+01 9.619122e+00
LAS1L 3.794109e+01 5.127040e+01 3.951027e+01 4.150325e+01 3.632048e+01
ENPP4 7.664867e+00 3.636199e+00 6.709292e+00 4.058677e+00 5.970489e+00
SEMA3F 3.359767e+01 3.272579e+01 2.683717e+01 1.872229e+01 2.073087e+01
ANKIB1 2.491082e+01 1.563565e+01 2.564440e+01 1.754396e+01 2.545750e+01
CYP51A1 8.686850e+00 1.527203e+01 1.118215e+01 2.710149e+01 1.459453e+01
X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6 8.639512e+00 7.787759e+00 6.838519e+00 9.762750e+00 2.026897e+00
TNMD 3.277056e+00 9.461763e-01 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.241309e+01 1.936022e+01 8.703569e+00 1.320843e+01 3.378161e+00
SCYL3 3.277056e+00 3.202443e+00 2.362397e+00 1.091131e+01 4.053793e+00
C1orf112 7.944379e-01 6.550452e-01 1.119030e+00 0.000000e+00 0.000000e+00
FGR 2.065538e+01 4.250515e+01 4.457471e+01 2.584257e+01 1.361399e+02
CFH 3.773580e+00 2.183484e+00 1.616377e+00 1.148559e+00 1.351264e+00
FUCA2 1.529293e+01 1.120855e+01 1.131464e+01 1.607982e+01 3.411943e+01
GCLC 3.326709e+01 2.612902e+01 2.729191e+01 2.239690e+01 2.094460e+01
NFYA 3.426013e+01 4.075837e+01 2.934346e+01 1.320843e+01 1.520173e+01
STPG1 8.142988e+00 4.730882e+00 4.351785e+00 7.465632e+00 6.756322e+00
NIPAL3 1.022839e+01 1.200916e+01 1.317969e+01 5.742794e+00 1.553954e+01
LAS1L 4.160868e+01 3.901158e+01 2.654589e+01 2.699113e+01 4.459173e+01
ENPP4 2.979142e+00 5.240361e+00 4.227448e+00 3.445676e+00 2.702529e+00
SEMA3F 2.691158e+01 3.384400e+01 3.344657e+01 1.148559e+01 2.736311e+01
ANKIB1 1.588876e+01 1.826848e+01 1.603943e+01 5.168515e+00 1.655299e+01
CYP51A1 1.698111e+01 1.448378e+01 1.373921e+01 3.445676e+00 1.047230e+01
X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte
TSPAN6 2.361189e+01 1.381167e+00 5.865657e+00 4.855878e+00 5.007100e+00 1.204236e+00
TNMD 0.000000e+00 0.000000e+00 9.776094e-01 1.213970e+00 0.000000e+00 1.003530e-01
DPM1 1.453040e+01 8.632296e+00 1.309997e+01 1.532637e+01 1.301846e+01 5.118002e+00
SCYL3 4.994823e+00 0.000000e+00 5.865657e+00 3.034924e-01 1.859780e+00 2.007060e+00
C1orf112 4.540748e-01 0.000000e+00 1.173131e+00 1.213970e+00 3.576500e+00 1.605648e+00
FGR 2.406597e+01 1.022064e+02 9.013559e+01 7.966675e+01 1.437753e+02 5.814452e+02
CFH 4.540748e+00 2.417043e+00 5.865657e+00 6.069848e+00 1.430600e+00 2.107413e+00
FUCA2 1.316817e+01 1.173992e+01 1.544623e+01 8.042548e+00 1.630884e+01 2.017095e+01
GCLC 1.498447e+01 3.211214e+01 3.832229e+01 4.097147e+01 6.122968e+01 5.890720e+01
NFYA 2.088744e+01 3.556506e+01 3.187007e+01 4.294417e+01 3.848314e+01 5.118002e+01
STPG1 9.535572e+00 6.905837e-01 1.153579e+01 1.062223e+01 3.862620e+00 4.917296e+00
NIPAL3 1.680077e+01 1.622872e+01 7.625354e+00 2.063748e+01 1.859780e+01 1.334695e+01
LAS1L 3.178524e+01 4.695969e+01 6.178492e+01 5.220069e+01 6.366170e+01 4.696520e+01
ENPP4 2.270374e+00 7.941713e+00 3.128350e+00 2.579685e+00 8.583599e-01 1.605648e+00
SEMA3F 2.724449e+00 2.106280e+01 5.474613e+01 4.688957e+01 2.632304e+01 1.605648e+01
ANKIB1 2.815264e+01 1.726459e+01 2.737306e+01 2.215494e+01 2.989954e+01 2.308119e+01
CYP51A1 4.994823e+00 1.622872e+01 9.971616e+00 1.502287e+01 1.173092e+01 1.123953e+01
X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte
TSPAN6 0.000000e+00 7.092256e+00 0.000000e+00 2.811115e+00 6.511858e+00 2.097175e+00
TNMD 4.211673e-01 3.546128e-01 0.000000e+00 3.513893e-01 0.000000e+00 2.621468e-01
DPM1 1.095035e+01 6.737643e+00 5.841804e+00 7.379176e+00 1.172134e+01 2.123389e+01
SCYL3 4.632840e+00 3.900741e+00 2.596357e+00 1.405557e+00 5.860672e+00 2.097175e+00
C1orf112 0.000000e+00 0.000000e+00 4.543625e+00 1.054168e+00 0.000000e+00 2.359321e+00
FGR 9.560497e+01 3.546128e+01 4.290480e+02 4.139366e+02 2.031700e+02 6.343953e+01
CFH 1.895253e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.572881e+00
FUCA2 2.211128e+01 2.021293e+01 9.087250e+00 1.774516e+01 2.409387e+01 1.494237e+01
GCLC 2.295362e+01 1.312067e+01 5.257623e+01 5.885771e+01 4.753656e+01 2.306892e+01
NFYA 4.043206e+01 4.326276e+01 2.823539e+01 3.759866e+01 2.539625e+01 4.325423e+01
STPG1 2.316420e+00 2.836902e+00 4.543625e+00 0.000000e+00 9.116601e+00 2.359321e+00
NIPAL3 1.263502e+01 9.929158e+00 1.914813e+01 1.335279e+01 1.758202e+01 1.389378e+01
LAS1L 4.085322e+01 4.964579e+01 5.939167e+01 5.516813e+01 3.451285e+01 3.067118e+01
ENPP4 5.896342e+00 2.836902e+00 0.000000e+00 2.108336e+00 1.497727e+01 1.048587e+00
SEMA3F 1.137152e+01 6.737643e+00 9.736340e+00 1.546113e+01 1.823320e+01 1.913672e+01
ANKIB1 2.337478e+01 2.553212e+01 2.174449e+01 2.178614e+01 2.018676e+01 1.677740e+01
CYP51A1 6.949260e+00 1.808525e+01 6.815438e+00 7.730565e+00 0.000000e+00 9.961580e+00
X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte
TSPAN6 3.356292e+00 2.730114e+00 3.850280e+00 3.593039e+00 8.596257e+00 9.705544e-02
TNMD 4.475056e-01 0.000000e+00 4.052926e-01 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.253016e+01 1.467437e+01 1.205746e+01 1.225860e+01 1.124126e+01 1.116138e+01
SCYL3 9.621371e+00 3.412643e-01 3.546310e+00 3.522587e+00 3.570753e+00 2.523441e+00
C1orf112 4.475056e-01 2.047586e+00 4.154249e+00 2.818070e+00 7.935007e-01 1.844053e+00
FGR 1.018075e+01 1.979333e+01 1.509715e+02 2.305181e+02 2.697902e+01 3.838543e+02
CFH 1.454393e+00 8.531608e+00 1.215878e+00 1.549938e+00 2.248252e+00 0.000000e+00
FUCA2 1.364892e+01 2.081712e+01 2.259506e+01 1.261086e+01 1.454751e+01 1.543181e+01
GCLC 3.524107e+01 1.603942e+01 6.322565e+01 8.130132e+01 2.711127e+01 9.200856e+01
NFYA 3.210853e+01 4.095172e+01 5.126952e+01 5.805224e+01 2.697902e+01 6.755059e+01
STPG1 1.286579e+01 1.228552e+01 4.762188e+00 3.663491e+00 2.645002e+00 3.979273e+00
NIPAL3 2.080901e+01 9.214136e+00 2.411491e+01 2.064236e+01 9.257508e+00 3.561935e+01
LAS1L 5.381255e+01 5.118965e+01 4.306234e+01 4.360963e+01 3.504628e+01 5.173055e+01
ENPP4 4.027551e+00 6.825286e-01 4.863512e+00 4.297557e+00 6.612506e+00 4.076328e+00
SEMA3F 2.886411e+01 2.320597e+01 2.066992e+01 2.184004e+01 1.811827e+01 6.890936e+00
ANKIB1 3.703109e+01 3.378517e+01 2.452020e+01 2.867386e+01 2.645002e+01 1.087021e+01
CYP51A1 5.593820e+00 9.555401e+00 6.889975e+00 8.313306e+00 8.199507e+00 3.591051e+00
X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte
TSPAN6 1.339373e+00 2.620246e+00 3.098215e+00 3.459986e+00 0.000000e+00 4.200378e+00
TNMD 0.000000e+00 1.588028e-01 0.000000e+00 0.000000e+00 0.000000e+00 6.269221e-02
DPM1 6.929801e+00 9.845774e+00 1.206673e+01 7.284181e+00 5.960893e+00 1.003075e+01
SCYL3 5.182792e+00 3.890669e+00 4.402727e+00 3.642091e+00 4.967411e+00 4.451147e+00
C1orf112 3.202849e+00 1.905634e+00 3.016683e+00 1.638941e+00 1.490223e+00 4.200378e+00
FGR 3.780527e+02 1.392701e+02 1.022411e+02 1.358500e+02 1.316364e+02 2.121504e+02
CFH 5.241026e-01 1.429225e+00 3.668939e+00 7.284181e-01 0.000000e+00 4.200378e+00
FUCA2 1.956650e+01 2.040616e+01 1.386044e+01 8.558913e+00 1.043156e+01 2.031228e+01
GCLC 1.259011e+02 6.995264e+01 4.900072e+01 6.227975e+01 6.954375e+01 1.201810e+02
NFYA 5.858302e+01 3.954190e+01 3.986914e+01 3.769564e+01 5.215781e+01 4.344570e+01
STPG1 4.891624e+00 7.622535e+00 4.647323e+00 7.284181e-01 4.967411e-01 5.078069e+00
NIPAL3 3.377550e+01 2.977553e+01 1.932308e+01 2.968304e+01 3.228817e+01 2.357227e+01
LAS1L 6.493049e+01 4.597341e+01 5.397417e+01 5.535978e+01 4.520344e+01 5.090607e+01
ENPP4 6.114530e+00 4.764084e+00 4.891919e+00 2.367359e+00 0.000000e+00 3.259995e+00
SEMA3F 4.775157e+00 2.255000e+01 2.584564e+01 3.605670e+01 1.142504e+01 1.899574e+01
ANKIB1 2.300228e+01 2.445563e+01 2.225823e+01 2.786199e+01 1.589571e+01 2.294535e+01
CYP51A1 5.823362e+00 1.032218e+01 9.213113e+00 2.003150e+00 1.986964e+00 5.328838e+00
X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte X158_Hip_sclerotic_adipocyte
TSPAN6 1.632528e+00 7.040817e+00 1.150174e+01
TNMD 2.098965e+00 0.000000e+00 0.000000e+00
DPM1 1.306022e+01 1.920223e+00 1.461032e+01
SCYL3 7.229767e+00 6.400743e+00 8.704023e+00
C1orf112 6.996549e-01 0.000000e+00 2.331435e+00
FGR 1.604542e+02 3.456401e+01 3.559324e+01
CFH 0.000000e+00 0.000000e+00 2.642293e+00
FUCA2 1.306022e+01 6.400743e-01 1.507661e+01
GCLC 5.457308e+01 6.144713e+01 3.947896e+01
NFYA 4.711010e+01 5.120594e+00 4.010068e+01
STPG1 3.964711e+00 0.000000e+00 1.305603e+01
NIPAL3 1.166091e+01 1.024119e+01 1.025831e+01
LAS1L 4.081320e+01 5.120594e+01 4.600698e+01
ENPP4 8.395859e+00 0.000000e+00 3.108579e-01
SEMA3F 2.448792e+01 5.888683e+01 3.543781e+01
ANKIB1 2.565401e+01 1.408163e+01 3.978982e+01
CYP51A1 5.364021e+00 1.152134e+01 2.253720e+01
[ reached getOption("max.print") -- omitted 22996 rows ]
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) patientX104 patientX105 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149 patientX150
TSPAN6 -11.81261 -0.48479544 0.4799604 -0.2372331 0.3982336 -0.8313460 -0.61786914 -0.10378028 -1.4153849 -0.1958023 -0.5294125 -0.1017646 -0.7996911 -0.5949694 0.1148174 0.5806153 3.250771e-01
TNMD -16.88876 -0.80307457 4.7493835 3.6948424 2.4478087 1.0673836 2.57413713 -0.59587521 2.1922774 -0.6626219 1.9760162 0.4995742 1.9331888 1.6649122 2.2137261 3.5097190 -2.549059e-15
DPM1 -11.50302 0.21432770 -0.3454353 0.3480624 0.4058605 -0.1072695 -0.11985162 0.10072213 -0.4111277 0.1650724 0.5092445 0.2155536 0.3007711 0.1913979 0.6848698 0.1692601 1.171145e-01
SCYL3 -11.20402 -0.32264134 -0.6152666 -1.4438349 -1.3935654 -1.7050781 -0.95047190 -1.18119375 -1.7421457 -2.1680747 -1.1105934 -1.0900598 -0.9254745 -1.1144629 -1.3550943 -0.7102205 -9.167936e-01
C1orf112 -17.77735 0.08551583 0.0348957 4.1129396 4.8517373 4.8924915 0.05207893 0.05687388 4.9668596 3.0131425 4.1636040 4.2636889 4.0891881 5.1817388 4.6093492 2.8014721 3.670812e+00
patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX99 groupsclerotic
TSPAN6 -1.68209474 -2.1154283 -0.84820389 -1.2799761 -0.07027376 -0.1289854 -0.8446642 0.3545509 0.3235262 0.3733027 0.0748689 -0.21224373 1.1597247 -1.66507892 -0.174245174
TNMD -0.67750790 -0.3584921 0.96831960 -0.6152991 -0.64836657 2.9788467 3.9069215 -0.2293990 3.8716593 4.4995441 2.4184572 -0.37110727 -0.8030746 -0.80307457 -0.803074569
DPM1 0.62995734 -0.1068463 0.08775776 -0.4070299 0.19993602 -0.1724064 0.1359955 -0.1170109 0.1315259 0.2295348 0.3322944 -0.22349279 0.3651815 -0.15457785 -0.008168107
SCYL3 -1.37708650 -0.9588707 -0.94422319 -0.9177319 -1.99936756 -1.2437641 -0.5813295 -0.3139428 -1.4989824 -1.3289580 -1.3827485 -0.46676433 -0.9989474 -6.48781839 -0.416132542
C1orf112 0.06737776 4.8440978 4.81957552 4.3886832 2.57888114 3.6348894 4.8726564 4.1750433 2.7178726 3.6278944 3.8138792 0.03144956 3.2169856 0.08551583 0.085515829
23008 more rows ...
$fitted.values
X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6 1.800000e+01 1.200000e+01 1.668800e+01 1.981073e+01 47.934152 40.7647533
TNMD 3.069639e-09 2.791350e-09 8.083928e+00 4.003878e+00 2.275506 0.8073838
DPM1 2.900000e+01 3.300000e+01 9.954496e+00 1.394775e+01 65.883642 66.1311608
SCYL3 2.600000e+01 2.600000e+01 1.025451e+01 9.520703e+00 14.634147 9.7334062
C1orf112 1.840681e-08 1.672647e-08 8.416104e-09 1.301153e-08 10.467413 11.5931102
X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6 1.449343e+01 5.739670e+00 2.177644e+01 4.944339e+00 92.8496869 47.3984671
TNMD 3.198689e-09 5.285061e-10 4.999326e-09 4.735819e-10 0.7138543 0.1520392
DPM1 2.427451e+01 1.134632e+01 4.265606e+01 1.143118e+01 174.1327125 104.9187216
SCYL3 9.063175e+00 2.807074e+00 5.515607e+00 9.794278e-01 63.5167672 25.3588708
C1orf112 1.330753e-08 6.863320e-09 1.321964e+00 3.908965e-01 18.5006337 12.2996087
X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6 50.229711 4.61712943 61.049536 31.8880249 2.949810e+00 6.168506e-01
TNMD 2.505426 0.09608491 7.164189 1.5612572 2.921631e-09 2.549021e-10
DPM1 121.295707 13.15968722 55.149366 33.9996581 4.113865e+01 1.015371e+01
SCYL3 21.167203 1.52171219 30.882363 12.6157610 7.421578e+00 1.213780e+00
C1orf112 11.466970 1.37271657 1.345312 0.9151433 1.340134e-08 3.649683e-09
X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6 5.696590e+01 1.245276e+01 50.813769 15.0008714 68.529011 65.576020
TNMD 1.197566e-08 1.092225e-09 7.111116 0.8758606 17.581948 7.019396
DPM1 1.019067e+02 2.629311e+01 66.377244 23.1282657 77.123823 87.105968
SCYL3 1.508364e+01 2.578780e+00 30.577258 7.0597821 20.239592 15.147119
C1orf112 1.923427e+00 5.475794e-01 5.495974 2.1130052 1.795816 2.237965
X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6 129.518018 90.879716 109.407627 107.630721 1.039545e+01 1.484962e+01
TNMD 61.889209 18.118151 6.797086 2.789803 3.084098e-09 1.838072e-09
DPM1 152.972552 126.689042 193.176061 224.300750 1.402735e+01 2.365029e+01
SCYL3 43.275243 23.748378 46.678623 35.914048 1.484502e+01 1.658481e+01
C1orf112 8.375582 7.653721 11.544490 14.790547 1.048149e-08 1.949916e-08
X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte
TSPAN6 5.200000e+01 4.000000e+00 29.777197 32.239676 22.3961831 26.8281783
TNMD 2.327208e-09 3.060380e-09 11.198430 5.058551 0.8461317 0.4228802
DPM1 3.200000e+01 2.500000e+01 73.055525 93.357385 63.2709574 89.4561808
SCYL3 1.100000e+01 1.728099e-07 16.314537 13.814630 17.1594974 16.0760523
C1orf112 1.000000e+00 1.833858e-08 5.833664 8.225629 17.5646048 27.4016298
X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte
TSPAN6 1.885374e+01 9.407993e+00 5.476127 8.4999953 6.6655817 13.9132196
TNMD 3.115819e+00 6.486851e-01 1.445280 0.9359646 0.5549299 0.4832701
DPM1 4.244578e+01 2.499901e+01 20.565932 37.6775215 25.7779132 63.5076604
SCYL3 2.492546e+01 9.727480e+00 7.281516 8.8394382 6.8575440 11.1947877
C1orf112 2.886827e-08 1.876036e-08 8.348386 16.8759607 1.8431623 5.0104186
X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte
TSPAN6 29.568123 8.1451796 40.11215 48.475480 6.500000e+01 8.975745e+00
TNMD 2.734187 0.3142442 2.16517 1.091693 7.990104e-09 1.800023e-08
DPM1 121.769418 39.5916778 120.50151 171.880838 8.500000e+01 9.330226e+01
SCYL3 48.046261 10.3512827 43.93949 41.529712 2.700000e+01 5.367082e+01
C1orf112 9.932282 3.5632541 33.17083 52.206362 6.000000e+00 2.462140e+01
X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte
TSPAN6 1.257031e+01 39.670966 32.4640180 1.120266e+01 3.450969e+00 50.43833
TNMD 1.051758e-08 1.215709 0.4150699 8.095297e-09 1.040435e-09 45.99004
DPM1 1.542255e+02 138.606364 133.8756016 3.680322e+01 1.338119e+01 184.23950
SCYL3 5.878564e+01 66.544738 42.5893378 2.979532e+01 7.178367e+00 121.36210
C1orf112 4.490647e+01 29.363663 31.2939628 8.289657e+00 3.325656e+00 39.32311
X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte X158_Hip_sclerotic_adipocyte
TSPAN6 11.393075 1.646668e+01 5.698149e+01
TNMD 4.334172 3.112427e-09 4.493544e-09
DPM1 49.119253 1.400652e+01 5.720666e+01
SCYL3 21.439813 1.554281e+01 4.206440e+01
C1orf112 11.567751 1.897504e+00 8.551283e+00
23008 more rows ...
$deviance
[1] 42.89574 17.54976 18.31456 25.97746 18.86381
23008 more elements ...
$iter
[1] 9 20 6 18 19
23008 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
23008 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6 18 12 26 9 43 45
TNMD 0 0 10 3 4 0
DPM1 29 33 6 19 70 62
SCYL3 26 26 14 6 10 13
C1orf112 0 0 0 0 1 22
X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6 16 5 28 3 65 62
TNMD 0 0 0 0 1 0
DPM1 34 6 38 13 174 105
SCYL3 4 5 8 0 50 31
C1orf112 0 0 2 0 16 14
X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6 33 7 59 33 4 0
TNMD 3 0 13 0 0 0
DPM1 101 16 66 27 26 15
SCYL3 18 2 12 21 11 0
C1orf112 19 0 0 2 0 0
X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6 43 16 75 7 66 68
TNMD 0 0 12 0 8 11
DPM1 96 28 59 26 79 85
SCYL3 21 1 38 5 36 3
C1orf112 3 0 10 0 2 2
X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6 135 87 107 110 17 6
TNMD 12 33 13 0 0 0
DPM1 155 125 266 140 23 10
SCYL3 27 33 44 38 19 12
C1orf112 8 8 9 18 0 0
X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte
TSPAN6 52 4 30 32 35 12
TNMD 0 0 5 8 0 1
DPM1 32 25 67 101 91 51
SCYL3 11 0 30 2 13 20
C1orf112 1 0 6 8 25 16
X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte
TSPAN6 0 20 0 16 10 8
TNMD 2 1 0 2 0 1
DPM1 52 19 18 42 18 81
SCYL3 22 11 8 8 9 8
C1orf112 0 0 14 6 0 9
X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte
TSPAN6 30 8 38 51 65 1
TNMD 4 0 4 0 0 0
DPM1 112 43 119 174 85 115
SCYL3 86 1 35 50 27 26
C1orf112 4 6 41 40 6 19
X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte
TSPAN6 23 33 38 19 0 67
TNMD 0 2 0 0 0 1
DPM1 119 124 148 40 12 160
SCYL3 89 49 54 20 10 71
C1orf112 55 24 37 9 3 67
X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte X158_Hip_sclerotic_adipocyte
TSPAN6 7 11 74
TNMD 9 0 0
DPM1 56 3 94
SCYL3 31 10 56
C1orf112 3 0 15
23008 more rows ...
$unshrunk.coefficients
(Intercept) patientX104 patientX105 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149 patientX150
TSPAN6 -11.81618 -0.4857755 0.4815589 -0.2376713 0.3996172 -0.8349319 -0.62049230 -0.10364519 -1.4242652 -0.1958416 -0.5313343 -0.1017497 -0.8029949 -0.5970923 0.1153811 0.5823536 0.326003704
TNMD -33.43411 -1.0494932 21.3746761 20.4022888 18.9699210 17.5070267 19.19721780 -0.71993593 18.8615692 -0.7727034 18.6007244 16.6481213 18.4340716 18.1016566 18.7351626 20.0576922 -0.001367914
DPM1 -11.50502 0.2146616 -0.3462706 0.3486418 0.4065154 -0.1075598 -0.12013989 0.10092276 -0.4121912 0.1653354 0.5100628 0.2159223 0.3012737 0.1917270 0.6858420 0.1695494 0.117343619
SCYL3 -11.20267 -0.3260937 -0.6189212 -1.4528657 -1.4003615 -1.7147787 -0.95482187 -1.18662893 -1.7528323 -2.1825964 -1.1164502 -1.0949358 -0.9310356 -1.1194661 -1.3622807 -0.7126548 -0.920271480
C1orf112 -32.78125 0.0881163 0.0388218 19.0973027 19.8431275 19.8871350 0.04734518 0.05279574 19.9624765 17.9675199 19.1482629 19.2501450 19.0711701 20.1779711 19.6033168 17.7323656 18.644293046
patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX99 groupsclerotic
TSPAN6 -1.69319335 -2.1372783 -0.85195087 -1.2863545 -0.07016719 -0.1288612 -0.8480978 0.3558369 0.3247568 0.3746516 0.0754737 -0.21260239 1.1624193 -1.67640213 -0.174008023
TNMD -0.80812864 -0.5467559 17.28068609 -0.7165589 -0.73508057 19.5225599 20.6775048 -0.4154361 20.5823017 21.2541067 18.9148164 -0.53304780 -1.0494915 -1.04949397 -1.048156435
DPM1 0.63085027 -0.1071237 0.08790375 -0.4080840 0.20027378 -0.1728381 0.1362234 -0.1171433 0.1317481 0.2299263 0.3328313 -0.22412561 0.3657476 -0.15498446 -0.008247751
SCYL3 -1.38405040 -0.9624428 -0.94820405 -0.9216624 -2.01251730 -1.2502801 -0.5835787 -0.3154125 -1.5083677 -1.3350958 -1.3898287 -0.46981412 -1.0044373 -19.24727852 -0.419791314
C1orf112 0.06222665 19.8368834 19.81225914 19.3775746 17.50656019 18.6120588 19.8680347 19.1601089 17.6480311 18.6012238 18.7916730 0.03744615 18.1762472 0.08811633 0.090146465
23008 more rows ...
$df.residual
[1] 25 25 25 25 25
23008 more elements ...
$design
(Intercept) patientX104 patientX105 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148
X102_tibia_sclerotic_adipocyte 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X104_tibia_non.sclerotic_adipocyte 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
X105_tibia_non.sclerotic_adipocyte 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
X105_tibia_sclerotic_adipocyte 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
X109_tibia_non.sclerotic_adipocyte 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
patientX149 patientX150 patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164
X102_tibia_sclerotic_adipocyte 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X104_tibia_non.sclerotic_adipocyte 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X105_tibia_non.sclerotic_adipocyte 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X105_tibia_sclerotic_adipocyte 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X109_tibia_non.sclerotic_adipocyte 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
patientX99 groupsclerotic
X102_tibia_sclerotic_adipocyte 0 1
X104_tibia_non.sclerotic_adipocyte 0 0
X105_tibia_non.sclerotic_adipocyte 0 0
X105_tibia_sclerotic_adipocyte 0 1
X109_tibia_non.sclerotic_adipocyte 0 0
52 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 14.88056 14.78686 14.14931 14.49485 15.28639 15.29839 14.59352 13.84123 15.09285 13.78427 16.44891 15.95053 15.6174 13.40458 15.34551 14.87006 14.59111 13.20025 15.9288 14.5823 15.87321 14.82716 15.71868 15.84864
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 16.30535 16.12507 16.43579 16.59342 14.37015 14.90076 14.605 14.87888 15.44759 15.70106 15.76 16.11457 15.37338 14.85224 14.94084 15.55452 14.24447 15.15436 16.00587 14.89061 16.10495 16.46834 15.83857 16.14798
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] 16.6588 16.34875 16.32227 15.51868 14.5152 16.58503 15.27129 14.26168 15.67708
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 57
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23008 more rows ...
$dispersion
[1] 0.3697942 2.0625567 0.2254943 0.5069176 1.1407601
23008 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 2.6401182 -0.2538736 3.5734554 2.0828518 0.7060840
23008 more elements ...
$df.residual.zeros
[1] 25 17 25 25 20
23008 more elements ...
$df.prior
[1] 33.27426 33.27426 33.27426 33.27426 33.27426
23008 more elements ...
$var.post
[1] 1.467260 1.216406 0.958906 1.210280 1.203960
23008 more elements ...
$var.prior
[1] 1.280502 1.310447 1.128950 1.338895 1.360699
23008 more elements ...
$samples52 more rows ...
$genes23008 more rows ...
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.707195
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.8389657
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.578436
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.353039
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.933007 2.933007
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 1.0733833 0.7937281
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic$boxplot_gg
$bone_hip_vs_tibia
$bone_hip_vs_tibia$name
[1] "tibia-vs-hip"
$bone_hip_vs_tibia$results
Coefficient: grouptibia
$bone_hip_vs_tibia$colsums_samples
$bone_hip_vs_tibia$normalized_matrix
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6 2.482204e-01 6.436249e+00 9.248072e+00 4.467957e+00 5.313580e+00 1.911082e+01
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 3.125635e-01 7.350317e+00
DPM1 1.464500e+01 1.036951e+01 1.387211e+01 1.228688e+01 1.781612e+01 4.410190e+00
SCYL3 5.047148e+00 9.296804e+00 3.302883e+00 9.680573e+00 2.187945e+00 1.029044e+01
C1orf112 5.874549e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.813072e+00 0.000000e+00
FGR 1.105574e+03 4.147805e+01 2.057696e+02 1.355280e+02 1.184616e+02 2.352101e+01
CFH 7.446611e-01 1.430278e+00 3.633171e+00 4.095627e+00 1.562818e+00 1.470063e+00
FUCA2 1.141814e+01 2.789041e+01 1.915672e+01 1.228688e+01 5.938707e+00 4.410190e+00
X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6 4.724198e+00 1.058919e+01 1.066013e+01 7.157967e+00 7.291801e+00 7.286609e+00
TNMD 1.574733e+00 9.850405e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.973307e+00 1.723821e+01 1.468730e+01 7.157967e+00 1.549508e+01 1.486468e+01
SCYL3 3.149465e+00 2.462601e+00 3.079594e+00 6.507243e+00 1.822950e+00 2.331715e+00
C1orf112 0.000000e+00 2.462601e-01 5.211621e+00 0.000000e+00 0.000000e+00 5.829287e-01
FGR 6.876333e+01 4.211048e+01 8.646554e+01 7.288112e+01 3.828196e+01 1.614713e+02
CFH 6.823842e+00 4.432682e+00 5.448513e+00 2.602897e+00 1.822950e+00 6.800835e-01
FUCA2 1.364768e+01 1.255927e+01 1.847757e+01 1.800337e+01 2.050819e+01 1.097849e+01
X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6 4.734692e+00 3.518309e+00 7.830008e+00 4.854921e-01 3.040348 1.416696e+01
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000 0.000000e+00
DPM1 5.681631e+00 1.348685e+01 1.062644e+01 1.929831e+01 13.174842 2.990802e+01
SCYL3 4.734692e+00 3.518309e+00 2.237145e+00 1.941968e+00 0.000000 1.101875e+01
C1orf112 0.000000e+00 0.000000e+00 5.592863e-01 2.791580e+00 0.000000 0.000000e+00
FGR 3.314285e+01 8.385302e+01 2.262313e+02 4.038081e+02 202.689872 8.972407e+01
CFH 0.000000e+00 4.104693e+00 1.118573e+00 7.282382e-01 4.053797 6.296426e+00
FUCA2 1.609795e+01 2.052347e+01 1.118573e+01 1.189456e+01 12.161392 3.148213e+00
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6 4.639200e+00 2.580648e+00 7.499628e+00 6.431380e+00 5.360471e+00 7.804782e-01
TNMD 7.137230e-02 0.000000e+00 0.000000e+00 2.046348e+00 4.873156e-01 0.000000e+00
DPM1 1.241878e+01 2.163774e+01 1.270098e+01 1.315510e+01 1.640629e+01 1.634413e+01
SCYL3 3.568615e+00 3.771716e+00 3.749814e+00 5.554374e+00 2.923893e+00 1.698688e+00
C1orf112 1.141957e+00 3.672461e+00 1.693464e+00 1.169342e+00 3.086332e+00 3.443286e+00
FGR 2.280345e+02 3.479905e+02 1.140669e+02 4.882002e+01 2.441451e+02 6.137313e+02
CFH 1.784308e+00 3.970228e-01 2.661158e+00 4.677367e+00 3.248770e-01 2.754629e-01
FUCA2 1.527367e+01 1.826305e+01 1.657176e+01 4.969703e+00 1.575654e+01 9.182096e+00
X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6 9.860365e+00 1.324182e+01 8.053954e+00 11.979693 9.741978 1.860788e+00
TNMD 0.000000e+00 2.917689e+00 0.000000e+00 0.000000 0.000000 0.000000e+00
DPM1 2.253798e+01 1.481288e+01 1.073861e+01 9.801567 0.000000 1.209512e+01
SCYL3 2.817247e+00 2.693252e+00 2.147721e+00 7.623441 1.391711 5.117167e+00
C1orf112 0.000000e+00 0.000000e+00 0.000000e+00 0.726042 0.000000 0.000000e+00
FGR 4.423078e+02 5.476279e+01 1.310110e+02 55.542213 89.069514 3.349419e+01
CFH 0.000000e+00 5.835379e+00 7.517024e+00 4.719273 27.834223 5.582364e+00
FUCA2 4.225871e+00 1.773057e+01 6.443163e+00 16.698966 11.133689 2.930741e+01
X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6 1.245728e+01 0.00000 4.880715e+01 5.603605e+00 8.240529e+00 7.565327e+00
TNMD 0.000000e+00 0.00000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.423689e+01 27.28395 4.880715e+00 1.251037e+01 1.278703e+01 1.323932e+01
SCYL3 6.821844e+00 0.00000 6.507621e+00 2.736644e+00 0.000000e+00 4.728329e-01
C1orf112 1.186408e+00 0.00000 0.000000e+00 3.909492e-01 8.524686e-01 0.000000e+00
FGR 5.398155e+01 156.42798 3.253810e+01 6.137902e+01 1.344059e+02 5.484862e+01
CFH 2.966019e+00 9.09465 1.626905e+01 2.345695e+00 1.136625e+00 6.146828e+00
FUCA2 1.571990e+01 14.55144 0.000000e+00 1.498639e+01 7.103905e+00 2.695148e+01
X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6 3.858497e+00 1.001714e+01 2.983326e+01 2.639900e+00 1.480583e+01 1.058055e+01
TNMD 0.000000e+00 1.602742e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.282491e+00
DPM1 1.234719e+01 7.880147e+00 1.376920e+01 9.805344e+00 2.035802e+01 1.266460e+01
SCYL3 7.716993e-01 5.075349e+00 4.589733e+00 1.885643e+00 9.253645e-01 5.771208e+00
C1orf112 0.000000e+00 1.335618e+00 1.147433e+00 0.000000e+00 9.253645e-01 3.206227e-01
FGR 8.874542e+01 3.926717e+01 5.622423e+01 2.753039e+01 7.773062e+01 2.084047e+01
CFH 1.080379e+01 5.342473e-01 8.032033e+00 1.131386e+00 9.253645e-01 2.244359e+00
FUCA2 5.401895e+00 1.856509e+01 2.868583e+01 7.919701e+00 9.253645e+00 1.811518e+01
X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6 5.356113e+00 9.311914e+00 6.753413e+00 1.242409e+01 4.302415e+00 9.320130e+00
TNMD 4.057661e-01 1.506339e+00 0.000000e+00 1.104363e+00 0.000000e+00 3.535222e+00
DPM1 1.217298e+01 1.163989e+01 1.000506e+01 1.426469e+01 1.916530e+01 1.339099e+01
SCYL3 2.109984e+00 4.108197e-01 3.751896e+00 2.484817e+00 5.475801e+00 3.535222e+00
C1orf112 4.869193e-01 2.738798e-01 2.501264e-01 7.362421e-01 4.302415e+00 8.570235e-01
FGR 6.029684e+01 2.998984e+01 3.576808e+01 1.546109e+01 3.441932e+01 2.228261e+01
CFH 3.164976e+00 2.191039e+00 3.001517e+00 2.392787e+00 7.040316e+00 4.070862e+00
FUCA2 1.671756e+01 1.999323e+01 2.976504e+01 1.794590e+01 1.486289e+01 1.649770e+01
X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6 3.324255e+00 7.937026e+00 1.962340e+01 7.050759e+00 1.610544e+01 1.010132e+01
TNMD 0.000000e+00 9.643116e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.007350e+01 1.973130e+01 8.176417e+00 8.973693e+00 1.030748e+01 1.366649e+01
SCYL3 4.029399e+00 3.263824e+00 9.811700e+00 2.435717e+00 2.576871e+00 1.128971e+01
C1orf112 6.044099e-01 6.676003e-01 0.000000e+00 1.153761e+00 1.288436e+00 0.000000e+00
FGR 4.533074e+01 4.331984e+01 8.421709e+01 4.595813e+01 6.012699e+01 2.673878e+01
CFH 5.338954e+00 2.225334e+00 8.176417e-01 1.666543e+00 2.147393e-01 1.188390e+00
FUCA2 1.017423e+01 1.142338e+01 2.943510e+01 1.166580e+01 2.405080e+01 1.663746e+01
X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6 1.515445e+00 2.090730e+00 2.471578e+01 1.362647e+01 5.996059e+00 1.432008e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.262871e+01 3.484550e+00 1.520971e+01 1.132046e+01 9.593694e+00 8.950050e+00
SCYL3 2.020593e+00 4.181460e+00 5.228339e+00 3.354209e+00 5.036689e+00 0.000000e+00
C1orf112 0.000000e+00 0.000000e+00 4.753035e-01 1.257828e+00 0.000000e+00 0.000000e+00
FGR 6.819501e+01 1.404274e+02 2.519109e+01 4.402399e+01 4.485052e+01 1.059686e+02
CFH 9.597816e+00 1.393820e+00 4.753035e+00 5.031313e+00 3.117951e+00 2.506014e+00
FUCA2 5.051482e+00 3.519395e+01 1.378380e+01 1.299756e+01 2.518345e+01 1.217207e+01
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet
TSPAN6 9.936018e+00 7.383362e+00 5.878601e+00 3.639067e+00 4.969456e+00 3.750479e+00
TNMD 0.000000e+00 0.000000e+00 9.797668e-01 0.000000e+00 1.242364e+00 0.000000e+00
DPM1 2.692340e+01 3.164298e+01 1.312887e+01 1.637580e+01 1.568485e+01 2.488954e+01
SCYL3 1.923100e+00 1.054766e+00 5.878601e+00 9.097668e+00 3.105910e-01 3.409526e-01
C1orf112 0.000000e+00 0.000000e+00 1.175720e+00 6.368368e+00 1.242364e+00 0.000000e+00
FGR 1.233989e+02 9.703847e+01 9.033450e+01 2.183440e+02 8.153014e+01 2.557145e+02
CFH 1.282067e+01 1.054766e+01 5.878601e+00 5.458601e+00 6.211820e+00 3.409526e-01
FUCA2 1.923100e+01 0.000000e+00 1.548032e+01 2.729300e+00 8.230662e+00 1.363811e+01
X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet
TSPAN6 4.835611e+00 1.588181e+00 1.121909e+00 7.915673e-01 0.000000e+00 0.000000e+00
TNMD 0.000000e+00 0.000000e+00 9.349240e-02 0.000000e+00 4.182015e-01 0.000000e+00
DPM1 1.257259e+01 9.869409e+00 4.768112e+00 1.675484e+01 1.087324e+01 9.276729e-01
SCYL3 1.796084e+00 4.537659e+00 1.869848e+00 5.013260e+00 4.600217e+00 1.298742e+01
C1orf112 3.454008e+00 4.537659e+00 1.495878e+00 4.221692e+00 0.000000e+00 0.000000e+00
FGR 1.388511e+02 4.116791e+02 5.416950e+02 4.432777e+02 9.493175e+01 1.363679e+02
CFH 1.381603e+00 3.403244e-01 1.963340e+00 1.055423e+00 1.881907e+00 0.000000e+00
FUCA2 1.575028e+01 1.134415e+01 1.879197e+01 8.179529e+00 2.195558e+01 2.783019e+00
X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet
TSPAN6 7.206997e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.810612e+00 2.263747e-01
TNMD 3.603499e-01 0.000000e+00 0.000000e+00 0.000000e+00 3.513265e-01 0.000000e+00
DPM1 6.846648e+00 6.110164e+00 5.749153e+00 4.865723e+00 7.377856e+00 1.478982e+01
SCYL3 3.963849e+00 6.110164e+00 2.555179e+00 0.000000e+00 1.405306e+00 3.546537e+00
C1orf112 0.000000e+00 8.146886e+00 4.471564e+00 9.731446e+00 1.053979e+00 1.358248e+00
FGR 3.603499e+01 7.230361e+01 4.222434e+02 6.874571e+02 4.138626e+02 3.418258e+02
CFH 0.000000e+00 3.055082e+00 0.000000e+00 6.951033e-01 0.000000e+00 2.263747e-01
FUCA2 2.053994e+01 1.272951e+01 8.943127e+00 6.255929e+00 1.774199e+01 1.305428e+01
X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6 6.214414e+00 7.803588e-01 2.135330e+00 6.634222e-01 3.524965e+00 2.697025e+00
TNMD 0.000000e+00 1.418834e-01 2.669162e-01 0.000000e+00 4.699953e-01 0.000000e+00
DPM1 1.118595e+01 2.014745e+01 2.162021e+01 3.980533e+00 1.315987e+01 1.449651e+01
SCYL3 5.592973e+00 3.192377e+00 2.135330e+00 1.149932e+01 1.010490e+01 3.371282e-01
C1orf112 0.000000e+00 3.759911e+00 2.402246e+00 2.211407e-01 4.699953e-01 2.022769e+00
FGR 1.938897e+02 3.742175e+02 6.459372e+01 4.842982e+01 1.069239e+01 1.955343e+01
CFH 0.000000e+00 3.547086e-01 1.601497e+00 7.518784e+00 1.527485e+00 8.428205e+00
FUCA2 2.299333e+01 1.518153e+01 1.521422e+01 1.437415e+01 1.433486e+01 2.056482e+01
X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6 0.000000e+00 3.688823e+00 1.052198e+00 3.424994e+00 2.131069e+00 0.000000e+00
TNMD 0.000000e+00 3.882972e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.190837e+00 1.155184e+01 7.966645e+00 1.168527e+01 1.150777e+01 2.033724e+01
SCYL3 9.526693e+00 3.397600e+00 1.202513e+00 3.357837e+00 2.273140e+00 0.000000e+00
C1orf112 0.000000e+00 3.980046e+00 5.411306e+00 2.686270e+00 3.693852e+00 0.000000e+00
FGR 3.036633e+01 1.446407e+02 1.832328e+02 2.197369e+02 3.423917e+02 1.110726e+02
CFH 4.167928e+00 1.164891e+00 1.052198e+00 1.477448e+00 0.000000e+00 0.000000e+00
FUCA2 2.619841e+01 2.164757e+01 1.037167e+01 1.202106e+01 1.747476e+01 7.822014e+00
X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet
TSPAN6 8.878739e+00 2.318747e+00 9.320149e-02 6.223297e-01 1.286401e+00 7.309524e-01
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.161066e+01 9.274989e+00 1.071817e+01 1.397413e+01 6.655729e+00 8.527777e+00
SCYL3 3.688092e+00 1.159374e+01 2.423239e+00 3.960280e+00 4.977814e+00 5.360317e+00
C1orf112 8.195759e-01 7.729158e-01 1.770828e+00 3.677403e+00 3.076177e+00 4.629365e+00
FGR 2.786558e+01 2.705205e+01 3.686119e+02 2.232466e+02 3.631008e+02 2.378032e+02
CFH 2.322132e+00 2.318747e+01 0.000000e+00 5.657543e-02 5.033745e-01 1.705555e+00
FUCA2 1.502556e+01 2.318747e+01 1.481904e+01 1.239002e+01 1.879265e+01 1.145159e+01
X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte
TSPAN6 2.488515e+00 3.452583e-01 3.034350e+00 9.298885e-01 3.338082e+00 0.000000e+00
TNMD 1.508191e-01 0.000000e+00 0.000000e+00 3.099628e-01 0.000000e+00 0.000000e+00
DPM1 9.350785e+00 1.484611e+01 1.181799e+01 1.100368e+01 7.027541e+00 5.749777e+00
SCYL3 3.695068e+00 3.590687e+00 4.311971e+00 3.874535e+00 3.513770e+00 4.791481e+00
C1orf112 1.809829e+00 2.002498e+00 2.954499e+00 1.394833e+00 1.581197e+00 1.437444e+00
FGR 1.322684e+02 3.271668e+02 1.001335e+02 3.234462e+02 1.310636e+02 1.269742e+02
CFH 1.357372e+00 1.450085e+00 3.593309e+00 2.169740e+00 7.027541e-01 0.000000e+00
FUCA2 1.938026e+01 1.374128e+01 1.357472e+01 1.053874e+01 8.257361e+00 1.006211e+01
X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte
TSPAN6 0.00000 3.965551e+00 0.000000e+00 1.612206e+00 0.000000e+00 7.310093e+00
TNMD 0.00000 5.918733e-02 0.000000e+00 2.072836e+00 0.000000e+00 0.000000e+00
DPM1 8.97128 9.469973e+00 1.141130e+01 1.289765e+01 8.912964e+00 1.993662e+00
SCYL3 0.00000 4.202300e+00 1.951934e+00 7.139770e+00 3.183202e+00 6.645539e+00
C1orf112 0.00000 3.965551e+00 3.903867e+00 6.909454e-01 8.488538e-01 0.000000e+00
FGR 174.93997 2.002899e+02 4.035998e+02 1.584568e+02 3.637338e+02 3.588591e+01
CFH 11.21410 3.965551e+00 0.000000e+00 0.000000e+00 1.697708e+00 0.000000e+00
FUCA2 10.09269 1.917669e+01 1.981963e+01 1.289765e+01 1.676486e+01 6.645539e-01
X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 3.074225e+00 1.185821e+01 7.899248e+00 3.686534e+00 9.056043e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.048853e+01 1.506313e+01 9.163127e+00 1.622075e+01 2.150810e+01
SCYL3 4.882593e+00 8.973781e+00 4.739549e+00 2.506843e+00 1.132005e+00
C1orf112 5.425103e-01 2.403691e+00 9.479097e-01 4.423841e-01 1.981009e+00
FGR 1.495520e+02 3.669636e+01 1.248081e+02 9.228132e+02 4.301621e+01
CFH 3.797572e+00 2.724184e+00 8.531187e+00 5.898454e-01 8.490041e+00
FUCA2 9.946023e+00 1.554387e+01 1.390268e+01 1.061722e+01 2.688513e+01
[ reached getOption("max.print") -- omitted 23496 rows ]
$bone_hip_vs_tibia$fit
An object of class "DGEGLM"
$coefficients
(Intercept) batchpellet grouptibia
TSPAN6 -12.72969 -0.256260356 1.1966817
TNMD -15.03322 -1.813749224 0.9475336
DPM1 -11.46287 0.122429782 0.1902987
SCYL3 -12.37079 0.002562051 -0.1146220
C1orf112 -13.25280 0.470777685 -0.8890405
23499 more rows ...
$fitted.values
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6 91.332666 27.377600 22.8796365 26.292265 24.1770894 13.318326
TNMD 1.159694 2.174532 0.2905135 2.088327 0.3069878 1.057840
DPM1 173.450396 35.502804 43.4508504 34.095360 45.9148508 17.270977
SCYL3 45.548739 10.513496 11.4103598 10.096707 12.0574158 5.114479
C1orf112 13.695423 1.962532 3.4308240 1.884731 3.6253783 0.954709
X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6 18.649625 39.752242 41.324303 34.839070 21.480325 77.7818197
TNMD 1.481292 3.157418 3.282283 0.442368 1.706127 0.9876322
DPM1 24.184515 51.550027 53.588649 66.163080 27.855318 147.7159051
SCYL3 7.161795 15.265583 15.869283 17.374678 8.248835 38.7907628
C1orf112 1.336877 2.849594 2.962285 5.224153 1.539793 11.6634602
X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6 10.3379384 12.8872315 35.006727 62.2615782 9.6594779 4.80074018
TNMD 0.8211158 0.1636352 2.780494 0.7905644 0.7672274 0.06095725
DPM1 13.4060617 24.4742162 45.396125 118.2413245 12.5262457 9.11711353
SCYL3 3.9699561 6.4270230 13.443219 31.0506250 3.7094150 2.39418896
C1orf112 0.7410633 1.9324530 2.509417 9.3361848 0.6924286 0.71987570
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6 137.159538 76.1354449 80.929651 25.8500155 60.265211 164.600244
TNMD 10.894228 0.9667274 6.428033 0.3282297 4.786710 2.090006
DPM1 177.866142 144.5892652 104.948187 49.0919144 78.150895 312.593279
SCYL3 52.671754 37.9696952 31.078456 12.8917249 23.142936 82.088193
C1orf112 9.832125 11.4165847 5.801350 3.8762352 4.320043 24.681968
X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6 6.9496150 43.617422 14.074222 26.966461 5.4299171 21.043539
TNMD 0.5519900 3.464419 0.178707 2.141876 0.0689462 1.671434
DPM1 9.0121418 56.562327 26.728437 34.969645 10.3119870 27.288902
SCYL3 2.6687784 16.749882 7.018990 10.355611 2.7079673 8.081101
C1orf112 0.4981752 3.126665 2.110443 1.933060 0.8142214 1.508482
X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6 25.4781770 5.3819507 4.64493958 75.120182 26.5940931 20.703701
TNMD 0.3235083 0.4274745 0.05897897 5.966602 0.3376777 1.644442
DPM1 48.3857537 6.9792216 8.82123172 97.414567 50.5049965 26.848206
SCYL3 12.7062844 2.0667668 2.31648926 28.847514 13.2628057 7.950597
C1orf112 3.8204777 0.3857990 0.69651325 5.384904 3.9878104 1.484121
X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6 9.7925134 73.294837 6.58589606 25.957701 8.1663779 61.064875
TNMD 0.1243401 5.821620 0.08362421 2.061753 0.1036923 4.850225
DPM1 18.5970190 95.047490 12.50731342 33.661502 15.5088157 79.187885
SCYL3 4.8836485 28.146549 3.28446844 9.968229 4.0726744 23.450021
C1orf112 1.4683970 5.254057 0.98756158 1.860748 1.2245564 4.377366
X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6 93.118622 71.486766 30.2122266 106.371435 19.3206923 91.380382
TNMD 1.182371 5.678009 0.3836188 8.448809 0.2453239 7.258108
DPM1 176.842116 92.702815 57.3762149 137.940657 36.6920389 118.500516
SCYL3 46.439417 27.452217 15.0672139 40.848563 9.6354700 35.091726
C1orf112 13.963229 5.124447 4.5303530 7.625115 2.8971568 6.550498
X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6 75.017393 131.971959 9.2422837 152.72584 35.1909391 16.475047
TNMD 0.952531 10.482192 0.1173536 12.13062 0.4468358 1.308570
DPM1 142.465967 171.138978 17.5520745 198.05226 66.8313166 21.364559
SCYL3 37.412109 50.679629 4.6092420 58.64950 17.5501599 6.326717
C1orf112 11.248932 9.460259 1.3858895 10.94798 5.2769159 1.180995
X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6 14.9597209 28.093707 20.596085 36.0472527 31.5076799 27.344518
TNMD 0.1899506 2.231411 1.635894 0.4577088 0.4000678 2.171905
DPM1 28.4100928 36.431438 26.708651 68.4575468 59.8364177 35.459903
SCYL3 7.4605992 10.788494 7.909271 17.9772141 15.7132726 10.500792
C1orf112 2.2432248 2.013865 1.476407 5.4053209 4.7246075 1.960161
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6 23.5771682 7.16450497 15.001620 2.49429248 18.929187 6.6555416 21.27686
TNMD 0.2993703 0.09097107 1.316079 0.03498145 1.660641 0.0933413 1.86660
DPM1 44.7755370 13.60615296 53.540512 13.03687876 67.557928 34.7864131 75.93673
SCYL3 11.7582276 3.57302791 21.528253 4.64853875 27.164555 12.4037350 30.53361
C1orf112 3.5354195 1.07432456 8.832051 3.07184100 11.144366 8.1966192 12.52653
X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6 20.0034807 31.442319 17.20049 14.058379 2.44614735 8.1576767 4.45662220
TNMD 0.2805408 2.758407 0.24123 1.233329 0.03430623 0.7156658 0.06250233
DPM1 104.5518736 112.217070 89.90154 50.174102 12.78523939 29.1146016 23.29335623
SCYL3 37.2798923 45.121673 32.05605 20.174644 4.55881211 11.7067708 8.30567432
C1orf112 24.6352473 18.511345 21.18323 8.276728 3.01254797 4.8027492 5.48854432
X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte
TSPAN6 9.2036370 3.26458612 16.734394 30.0725872 4.7303217 31.9871686 11.0132605
TNMD 0.8074269 0.04578451 1.468094 0.4217559 0.4149869 0.4486072 0.9661836
DPM1 32.8476150 17.06296027 59.724752 157.1799122 16.8824332 167.1868245 39.3061287
SCYL3 13.2077885 6.08411212 24.014891 56.0453868 6.7883044 59.6135354 15.8047102
C1orf112 5.4185476 4.02049463 9.852204 37.0358357 2.7849288 39.3937347 6.4839450
X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6 10.2614503 25.018274 8.7195848 3.81114315 30.282146 15.0965546 43.772489
TNMD 0.1439127 2.194831 0.7649615 0.05344975 2.656626 0.2117231 3.840122
DPM1 53.6333586 89.289771 31.1200413 19.91964119 108.076436 78.9049216 156.223226
SCYL3 19.1239598 35.902772 12.5131437 7.10271421 43.456753 28.1350002 62.816230
C1orf112 12.6374689 14.729254 5.1335668 4.69360587 17.828305 18.5921322 25.770607
X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte
TSPAN6 15.9724409 2.9010746 21.520529 2.9359273 31.540459 40.1097168 52.558403
TNMD 0.2240071 0.0406864 1.887977 0.0411752 2.767017 0.5625227 4.610902
DPM1 83.4829026 15.1630002 76.806381 15.3451645 112.567330 209.6408177 187.579997
SCYL3 29.7673634 5.4066464 30.883291 5.4716005 45.262510 74.7512870 75.424561
C1orf112 19.6708283 3.5728127 12.669992 3.6157355 18.569124 49.3970430 30.943225
X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte
TSPAN6 9.3134299 38.982031 32.8627028 36.813643 29.2838277 16.731985 6.1350923
TNMD 0.1306171 3.419859 0.4608862 3.229628 0.4106939 1.467882 0.5382262
DPM1 48.6783556 139.126168 171.7629652 131.387230 153.0573157 59.716154 21.8960343
SCYL3 17.3571624 55.941626 61.2452425 52.829855 54.5753993 24.011434 8.8042371
C1orf112 11.4699363 22.950274 40.4719971 21.673658 36.0644405 9.850786 3.6119732
X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet
TSPAN6 2.02354574 49.666336 15.1131777 12.763458 10.6931234 4.4234451 12.5484680
TNMD 0.02837942 4.357184 0.2119562 1.119727 0.1499668 0.3880649 0.1759872
DPM1 10.57643427 177.258259 78.9918053 45.552553 55.8895776 15.7871960 65.5868780
SCYL3 3.77122205 71.274265 28.1659802 18.316352 19.9284562 6.3479174 23.3862069
C1orf112 2.49209378 29.240550 18.6126044 7.514356 13.1690951 2.6042583 15.4540412
X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 18.344396 7.1817741 15.388604 8.0184227
TNMD 1.609338 0.1007215 0.215819 0.1124552
DPM1 65.470819 37.5368644 80.431373 41.9097622
SCYL3 26.325343 13.3844590 28.679285 14.9436961
C1orf112 10.800076 8.8446998 18.951806 9.8750727
23499 more rows ...
$deviance
[1] 163.11534 57.67103 60.54948 81.65890 96.77025
23499 more elements ...
$iter
[1] 7 6 3 3 5
23499 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
23499 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6 3 18 28 12 17 26
TNMD 0 0 0 0 1 10
DPM1 177 29 42 33 57 6
SCYL3 61 26 10 26 7 14
C1orf112 71 0 0 0 9 0
X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6 9 43 45 33 16 75
TNMD 3 4 0 0 0 0
DPM1 19 70 62 33 34 153
SCYL3 6 10 13 30 4 24
C1orf112 0 1 22 0 0 6
X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6 5 6 28 4 3 9
TNMD 0 0 0 0 0 0
DPM1 6 23 38 159 13 19
SCYL3 5 6 8 16 0 7
C1orf112 0 0 2 23 0 0
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6 65 26 62 22 33 17
TNMD 1 0 0 7 3 0
DPM1 174 218 105 45 101 356
SCYL3 50 38 31 19 18 37
C1orf112 16 37 14 4 19 75
X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6 7 59 15 33 7 4
TNMD 0 13 0 0 0 0
DPM1 16 66 20 27 0 26
SCYL3 2 12 4 21 1 11
C1orf112 0 0 0 2 0 0
X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6 42 0 30 43 29 16
TNMD 0 0 0 0 0 0
DPM1 48 15 3 96 45 28
SCYL3 23 0 4 21 0 1
C1orf112 4 0 0 3 3 0
X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6 5 75 26 7 16 66
TNMD 0 12 0 0 0 8
DPM1 16 59 12 26 22 79
SCYL3 1 38 4 5 1 36
C1orf112 0 10 1 0 1 2
X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6 66 68 27 135 11 87
TNMD 5 11 0 12 0 33
DPM1 150 85 40 155 49 125
SCYL3 26 3 15 27 14 33
C1orf112 6 2 1 8 11 8
X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6 33 107 24 110 75 17
TNMD 0 13 0 0 0 0
DPM1 100 266 10 140 48 23
SCYL3 40 44 12 38 12 19
C1orf112 6 9 0 18 6 0
X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6 3 6 52 65 25 4
TNMD 0 0 0 0 0 0
DPM1 25 10 32 54 40 25
SCYL3 4 12 11 16 21 0
C1orf112 0 0 1 6 0 0
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6 31 7 30 4 32 11 35
TNMD 0 0 5 0 8 0 0
DPM1 84 30 67 18 101 73 91
SCYL3 6 1 30 10 2 1 13
C1orf112 0 0 6 7 8 0 25
X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6 14 12 6 0 0 20 0
TNMD 0 1 0 2 0 1 0
DPM1 87 51 127 52 1 19 12
SCYL3 40 20 38 22 14 11 12
C1orf112 40 16 32 0 0 0 16
X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte
TSPAN6 0 0 16 3 10 11 8
TNMD 0 0 2 0 0 2 1
DPM1 18 7 42 196 18 284 81
SCYL3 8 0 8 47 9 45 8
C1orf112 14 14 6 18 0 53 9
X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6 3 30 8 0 38 7 51
TNMD 0 4 0 0 4 0 0
DPM1 18 112 43 2 119 53 174
SCYL3 52 86 1 16 35 8 50
C1orf112 1 4 6 0 41 36 40
X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte
TSPAN6 15 0 65 3 1 11 23
TNMD 0 0 0 0 0 0 0
DPM1 81 26 85 12 115 247 119
SCYL3 16 0 27 15 26 70 89
C1orf112 26 0 6 1 19 65 55
X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte
TSPAN6 3 33 5 38 12 19 0
TNMD 0 2 0 0 4 0 0
DPM1 35 124 215 148 142 40 12
SCYL3 22 49 52 54 50 20 10
C1orf112 19 24 29 37 18 9 3
X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet
TSPAN6 0 67 0 7 0 11 17
TNMD 0 1 0 9 0 0 0
DPM1 8 160 76 56 42 3 58
SCYL3 0 71 13 31 15 10 27
C1orf112 0 67 26 3 4 0 3
X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 74 25 25 32
TNMD 0 0 0 0
DPM1 94 29 110 76
SCYL3 56 15 17 4
C1orf112 15 3 3 7
23499 more rows ...
$unshrunk.coefficients
(Intercept) batchpellet grouptibia
TSPAN6 -12.73723 -0.258841422 1.2030198
TNMD -15.17073 -2.092282454 1.1036096
DPM1 -11.46495 0.122655226 0.1906258
SCYL3 -12.37602 0.002498425 -0.1152536
C1orf112 -13.26700 0.479201439 -0.9026990
23499 more rows ...
$df.residual
[1] 110 110 110 110 110
23499 more elements ...
$design
(Intercept) batchpellet grouptibia
X102_tibia_non.sclerotic_pellet 1 1 1
X102_tibia_sclerotic_adipocyte 1 0 1
X102_tibia_sclerotic_pellet 1 1 1
X104_tibia_non.sclerotic_adipocyte 1 0 1
X104_tibia_non.sclerotic_pellet 1 1 1
108 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 16.30756 14.84394 14.9233 14.80349 14.97846 14.12335 14.46004 15.21688 15.25566 15.34379 14.60135 16.14696 13.87003 14.34929 15.08975 15.9244 13.80215 13.36182 16.45536 16.12557 15.92779 15.04536 15.63297 16.89657
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 13.4729 15.30967 14.4374 14.82881 13.48498 14.5808 15.03087 13.21726 13.32883 15.8533 15.07374 14.56452 14.07467 15.8287 13.67798 14.79068 13.89308 15.64615 16.32693 15.80372 15.2013 16.20115 14.75423 16.04924
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72]
[1,] 16.11077 16.4168 14.01684 16.56286 15.35384 14.33606 14.49841 14.86976 14.55931 15.37788 15.24328 14.84273 14.95333 13.76219 15.44539 13.91008 15.67794 14.89152 15.79485 15.99198 16.18539 15.84101 15.38045 13.89059
[,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] 14.83619 14.49046 14.95683 14.17921 15.5547 16.39969 14.29122 16.46141 15.13633 15.32447 15.95684 14.9028 14.334 16.14779 15.71054 16.51624 15.76694 14.06115 15.80624 14.0731 16.1885 16.68769 16.69916 15.22753
[,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112] [,113]
[1,] 16.40033 16.48841 16.3431 16.37311 15.55455 14.55126 13.70092 16.64256 15.71164 15.28382 15.36567 14.22415 15.52567 15.64656 14.96762 15.7297 15.07781
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 113
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23499 more rows ...
$dispersion
[1] 0.6344835 5.7890991 0.4022576 0.8318417 1.7506890
23499 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 2.6271853 -0.6012498 3.6772455 2.1131351 0.9287606
23499 more elements ...
$df.residual.zeros
[1] 110 110 110 110 110
23499 more elements ...
$df.prior
[1] 13.36577 13.36577 13.36577 13.36577 13.36577
23499 more elements ...
$var.post
[1] 1.4305485 0.5396419 0.5795783 0.7766234 0.8972329
23499 more elements ...
$var.prior
[1] 0.9999703 0.6660528 0.8193053 1.0586628 1.0412855
23499 more elements ...
$samples108 more rows ...
$genes23499 more rows ...
$bone_hip_vs_tibia$mds_plot
$bone_hip_vs_tibia$mds_plot$rect
$bone_hip_vs_tibia$mds_plot$rect$w
[1] 0.8716978
$bone_hip_vs_tibia$mds_plot$rect$h
[1] 0.7661222
$bone_hip_vs_tibia$mds_plot$rect$left
[1] 3.131486
$bone_hip_vs_tibia$mds_plot$rect$top
[1] 1.929569
$bone_hip_vs_tibia$mds_plot$text
$bone_hip_vs_tibia$mds_plot$text$x
[1] 3.483424 3.483424
$bone_hip_vs_tibia$mds_plot$text$y
[1] 1.674194 1.418820
$bone_hip_vs_tibia$ql_disp_plot
NULL
$bone_hip_vs_tibia$boxplot_gg
$bone_non_sclerotic_hip_vs_tibia
$bone_non_sclerotic_hip_vs_tibia$name
[1] "tibia-vs-hip"
$bone_non_sclerotic_hip_vs_tibia$results
Coefficient: grouptibia
$bone_non_sclerotic_hip_vs_tibia$colsums_samples
$bone_non_sclerotic_hip_vs_tibia$normalized_matrix
X102_tibia_non.sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte
TSPAN6 2.544552e-01 4.556620e+00 5.441866e+00 1.875811e+01 1.016784e+01
TNMD 0.000000e+00 0.000000e+00 3.201097e-01 7.214659e+00 9.458457e-01
DPM1 1.501286e+01 1.253071e+01 1.824625e+01 4.328795e+00 1.655230e+01
SCYL3 5.173923e+00 9.872678e+00 2.240768e+00 1.010052e+01 2.364614e+00
C1orf112 6.022107e+00 0.000000e+00 2.880988e+00 0.000000e+00 2.364614e-01
FGR 1.133344e+03 1.382175e+02 1.213216e+02 2.308691e+01 4.043491e+01
CFH 7.633657e-01 4.176902e+00 1.600549e+00 1.442932e+00 4.256306e+00
FUCA2 1.170494e+01 1.253071e+01 6.082085e+00 4.328795e+00 1.205953e+01
GCLC 4.902504e+01 2.771944e+01 1.696582e+01 6.132460e+01 3.405045e+01
NFYA 5.776134e+01 5.354029e+01 3.969361e+01 3.463036e+01 2.080861e+01
STPG1 2.205279e+00 3.797184e-01 3.521207e+00 7.214659e-01 2.837537e+00
NIPAL3 1.781187e+01 4.176902e+00 5.121756e+00 1.659371e+01 3.310460e+00
LAS1L 5.046695e+01 8.771494e+01 7.394535e+01 3.535183e+01 4.800167e+01
ENPP4 1.314685e+01 2.278310e+00 3.201097e+00 7.214659e-01 6.384459e+00
SEMA3F 1.441913e+00 8.771494e+01 7.714645e+01 4.978114e+01 1.560645e+01
ANKIB1 7.718475e+00 1.215099e+01 1.280439e+01 1.298639e+01 1.418769e+01
CYP51A1 6.531018e+00 6.834931e+00 1.312450e+01 5.050261e+00 8.985535e+00
X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X144_Tibia_non.sclerotic_adipocyte
TSPAN6 7.355478e+00 7.415489e+00 8.034642e+00 5.017895e-01 4.775412e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 7.346787e-02
DPM1 1.563039e+01 1.512760e+01 1.090416e+01 1.994613e+01 1.278341e+01
SCYL3 1.838869e+00 2.372957e+00 2.295612e+00 2.007158e+00 3.673394e+00
C1orf112 0.000000e+00 5.932391e-01 5.739030e-01 2.885290e+00 1.175486e+00
FGR 3.861626e+01 1.643272e+02 2.321438e+02 4.173635e+02 2.347299e+02
CFH 1.838869e+00 6.921123e-01 1.147806e+00 7.526843e-01 1.836697e+00
FUCA2 2.068728e+01 1.117267e+01 1.147806e+01 1.229384e+01 1.572212e+01
GCLC 2.758304e+01 2.847548e+01 3.845150e+01 6.335093e+01 4.768065e+01
NFYA 1.700954e+01 3.450674e+01 2.812125e+01 3.826145e+01 3.173812e+01
STPG1 1.838869e+00 5.141406e+00 7.173788e+00 3.888869e+00 7.640659e+00
NIPAL3 1.287209e+01 1.750055e+01 1.836490e+01 1.806442e+01 1.564866e+01
LAS1L 3.631767e+01 5.111744e+01 3.012991e+01 4.014316e+01 3.680740e+01
ENPP4 2.298587e+00 8.404221e+00 1.492148e+01 6.021474e+00 2.791779e+00
SEMA3F 2.068728e+01 6.051039e+01 4.332968e+01 2.998193e+01 2.578722e+01
ANKIB1 1.471096e+01 1.750055e+01 1.262587e+01 1.041213e+01 1.234260e+01
CYP51A1 2.298587e+01 7.316616e+00 8.321594e+00 7.777738e+00 9.918163e+00
X144_Tibia_non.sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet
TSPAN6 2.661668e+00 5.592374e+00 8.147215e-01 1.296000e+01 8.290052e+00
TNMD 0.000000e+00 5.083976e-01 0.000000e+00 2.855593e+00 0.000000e+00
DPM1 2.231706e+01 1.711605e+01 1.706123e+01 1.449762e+01 1.105340e+01
SCYL3 3.890130e+00 3.050386e+00 1.773217e+00 2.635932e+00 2.210680e+00
C1orf112 3.787758e+00 3.219852e+00 3.594360e+00 0.000000e+00 0.000000e+00
FGR 3.589157e+02 2.547072e+02 6.406586e+02 5.359728e+01 1.348515e+02
CFH 4.094873e-01 3.389317e-01 2.875488e-01 5.711185e+00 7.737382e+00
FUCA2 1.883642e+01 1.643819e+01 9.584959e+00 1.735322e+01 6.632041e+00
GCLC 4.975271e+01 7.541231e+01 1.008817e+02 3.514576e+01 1.547476e+01
NFYA 3.900367e+01 4.423059e+01 5.147123e+01 3.185084e+01 6.079371e+00
STPG1 4.606733e+00 9.320623e+00 4.696630e+00 5.271863e+00 2.210680e+00
NIPAL3 1.863167e+01 1.525193e+01 1.888237e+01 9.006100e+00 8.842722e+00
LAS1L 4.862662e+01 3.796035e+01 5.818070e+01 3.536542e+01 3.260754e+01
ENPP4 8.087375e+00 4.745044e+00 3.019262e+00 1.252068e+01 2.210680e+00
SEMA3F 9.622953e+00 4.948403e+01 9.968357e+00 2.789694e+01 3.260754e+01
ANKIB1 7.370772e+00 1.711605e+01 8.243064e+00 1.383864e+01 6.632041e+00
CYP51A1 5.220964e+00 1.508246e+01 7.859666e+00 1.164203e+01 8.290052e+00
X151_Tibia_non.sclerotic_adipocyte X151_Tibia_non.sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte
TSPAN6 1.857733e+00 1.274811e+01 5.531746e+00 8.579585e+00 9.843050e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.574888e+00
DPM1 1.207527e+01 1.456926e+01 1.234994e+01 1.331315e+01 7.743200e+00
SCYL3 5.108767e+00 6.981106e+00 2.701550e+00 0.000000e+00 4.987145e+00
C1orf112 0.000000e+00 1.214105e+00 3.859358e-01 8.875433e-01 1.312407e+00
FGR 3.343920e+01 5.524179e+01 6.059192e+01 1.399360e+02 3.858476e+01
CFH 5.573200e+00 3.035263e+00 2.315615e+00 1.183391e+00 5.249627e-01
FUCA2 2.925930e+01 1.608690e+01 1.479420e+01 7.396194e+00 1.824245e+01
GCLC 2.925930e+01 1.456926e+01 3.910816e+01 1.597578e+01 3.320389e+01
NFYA 1.532630e+01 4.461837e+01 2.418531e+01 1.804671e+01 4.803409e+01
STPG1 1.253970e+01 1.153400e+01 6.174972e+00 8.875433e+00 9.843050e+00
NIPAL3 5.108767e+00 8.498738e+00 1.247859e+01 2.337197e+01 2.480449e+01
LAS1L 3.715467e+01 2.944206e+01 4.785604e+01 4.526471e+01 3.897848e+01
ENPP4 1.671960e+01 8.498738e+00 7.461425e+00 5.916955e-01 7.874440e+00
SEMA3F 1.904177e+01 4.704658e+01 1.698117e+01 4.467301e+01 3.451630e+01
ANKIB1 2.136393e+01 1.031990e+01 2.071189e+01 1.627163e+01 2.559193e+01
CYP51A1 1.857733e+00 6.677580e+00 8.747878e+00 1.212976e+01 8.924366e+00
X156_Tibia_non.sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte X159_Tibia_non.sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet
TSPAN6 3.127640e+01 1.009487e+01 5.524393e+00 1.179132e+01 4.367590e+00
TNMD 0.000000e+00 1.223620e+00 4.185146e-01 1.048118e+00 0.000000e+00
DPM1 1.443526e+01 1.208325e+01 1.255544e+01 1.353819e+01 1.945563e+01
SCYL3 4.811754e+00 5.506291e+00 2.176276e+00 2.358265e+00 5.558750e+00
C1orf112 1.202938e+00 3.059050e-01 5.022175e-01 6.987451e-01 4.367590e+00
FGR 5.894398e+01 1.988383e+01 6.219127e+01 1.467365e+01 3.494072e+01
CFH 8.420569e+00 2.141335e+00 3.264414e+00 2.270922e+00 7.146965e+00
FUCA2 3.007346e+01 1.728363e+01 1.724280e+01 1.703191e+01 1.508804e+01
GCLC 2.165289e+01 3.426136e+01 2.552939e+01 3.878035e+01 2.620554e+01
NFYA 4.571166e+01 2.860212e+01 2.954713e+01 3.397648e+01 3.295545e+01
STPG1 0.000000e+00 3.823813e+00 4.268849e+00 8.559628e+00 5.955804e+00
NIPAL3 2.044995e+01 8.871246e+00 1.322506e+01 1.013180e+01 4.764643e+00
LAS1L 2.285583e+01 4.053242e+01 3.599226e+01 3.825629e+01 2.580848e+01
ENPP4 0.000000e+00 6.882863e+00 5.105878e+00 6.288706e+00 1.270572e+01
SEMA3F 5.894398e+01 2.753145e+01 4.461366e+01 2.183578e+01 4.685233e+01
ANKIB1 4.811754e+00 2.630783e+01 1.799613e+01 2.681434e+01 1.548509e+01
CYP51A1 7.217630e+00 1.147144e+01 1.657318e+01 1.537239e+01 1.985268e+01
X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_adipocyte
TSPAN6 7.842766e+00 2.026926e+01 1.019627e+01 1.594616e+00 2.398367e+01
TNMD 9.528594e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.949697e+01 8.445525e+00 1.379496e+01 1.328846e+01 1.475918e+01
SCYL3 3.225062e+00 1.013463e+01 1.139583e+01 2.126154e+00 5.073468e+00
C1orf112 6.596719e-01 0.000000e+00 0.000000e+00 0.000000e+00 4.612244e-01
FGR 4.280537e+01 8.698891e+01 2.699014e+01 7.175770e+01 2.444489e+01
CFH 2.198906e+00 8.445525e-01 1.199562e+00 1.009923e+01 4.612244e+00
FUCA2 1.128772e+01 3.040389e+01 1.679386e+01 5.315385e+00 1.337551e+01
GCLC 2.631358e+01 3.040389e+01 2.339145e+01 8.504616e+00 1.522040e+01
NFYA 4.104625e+01 2.280292e+01 1.379496e+01 1.647769e+01 2.121632e+01
STPG1 4.764297e+00 1.942471e+01 7.797150e+00 3.189231e+00 9.685712e+00
NIPAL3 1.209398e+01 1.604650e+01 5.997808e+00 3.295539e+01 1.706530e+01
LAS1L 3.928712e+01 3.969397e+01 2.818970e+01 2.976616e+01 3.228571e+01
ENPP4 5.277375e+00 0.000000e+00 3.598685e+00 5.846924e+00 2.306122e+00
SEMA3F 3.408305e+01 4.391673e+01 1.199562e+01 3.189231e+01 2.767346e+00
ANKIB1 1.839752e+01 1.858016e+01 5.398027e+00 1.116231e+01 2.859591e+01
CYP51A1 1.458608e+01 1.942471e+01 3.598685e+00 1.435154e+01 5.073468e+00
X164_tibia_non.sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6 1.402975e+01 1.401284e+00 1.024725e+01 6.013240e+00 3.704418e+00 5.042266e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 1.002207e+00 0.000000e+00 0.000000e+00
DPM1 1.165548e+01 8.758023e+00 2.776673e+01 1.342957e+01 1.666988e+01 1.310989e+01
SCYL3 3.453476e+00 0.000000e+00 1.983338e+00 6.013240e+00 9.261044e+00 1.872842e+00
C1orf112 1.295053e+00 0.000000e+00 0.000000e+00 1.202648e+00 6.482731e+00 3.601619e+00
FGR 4.532687e+01 1.036950e+02 1.272642e+02 9.240345e+01 2.222651e+02 1.447851e+02
CFH 5.180214e+00 2.452246e+00 1.322225e+01 6.013240e+00 5.556626e+00 1.440647e+00
FUCA2 1.338222e+01 1.191091e+01 1.983338e+01 1.583486e+01 2.778313e+00 1.642338e+01
GCLC 1.769906e+01 3.257985e+01 1.388337e+01 3.928650e+01 2.222651e+01 6.165971e+01
NFYA 2.935454e+01 3.608306e+01 1.751949e+01 3.267194e+01 3.611807e+01 3.875342e+01
STPG1 5.396056e+00 7.006418e-01 0.000000e+00 1.182604e+01 2.778313e+00 3.889748e+00
NIPAL3 1.489311e+01 1.646508e+01 1.553615e+01 7.817212e+00 9.261044e+00 1.872842e+01
LAS1L 4.252092e+01 4.764365e+01 3.867509e+01 6.333946e+01 5.834458e+01 6.410881e+01
ENPP4 1.942580e+00 8.057381e+00 3.636120e+00 3.207061e+00 7.408835e+00 8.643885e-01
SEMA3F 4.295260e+01 2.136958e+01 4.131954e+01 5.612357e+01 3.704418e+01 2.650791e+01
ANKIB1 1.359806e+01 1.751605e+01 8.594465e+00 2.806179e+01 8.334939e+00 3.010953e+01
CYP51A1 1.165548e+01 1.646508e+01 2.247783e+01 1.022251e+01 8.334939e+00 1.181331e+01
X125_Hip_non.sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X143_Hip_non.sclerotic_adipocyte
TSPAN6 1.680567e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.789262e+00
TNMD 0.000000e+00 4.296881e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.044353e+01 1.117189e+01 9.507294e-01 6.034610e+00 4.975036e+00 1.222067e+01
SCYL3 4.801621e+00 4.726569e+00 1.331021e+01 2.682049e+00 0.000000e+00 6.110336e+00
C1orf112 4.801621e+00 0.000000e+00 0.000000e+00 4.693586e+00 9.950072e+00 0.000000e+00
FGR 4.356271e+02 9.753920e+01 1.397572e+02 4.432086e+02 7.029015e+02 2.118250e+02
CFH 3.601216e-01 1.933597e+00 0.000000e+00 0.000000e+00 7.107194e-01 0.000000e+00
FUCA2 1.200405e+01 2.255863e+01 2.852188e+00 9.387171e+00 6.396475e+00 2.512027e+01
GCLC 8.354821e+01 2.341800e+01 1.045802e+01 5.431149e+01 5.970043e+01 4.956161e+01
NFYA 7.502533e+01 4.125006e+01 2.376823e+01 2.916728e+01 4.122173e+01 2.647812e+01
STPG1 5.761946e+00 2.363285e+00 4.753647e+00 4.693586e+00 1.350367e+01 9.504966e+00
NIPAL3 1.752592e+01 1.289064e+01 3.232480e+01 1.978011e+01 1.421439e+01 1.833101e+01
LAS1L 6.566217e+01 4.167975e+01 5.133939e+01 6.135187e+01 5.898971e+01 3.598309e+01
ENPP4 3.121054e+00 6.015634e+00 0.000000e+00 0.000000e+00 1.421439e+00 1.561530e+01
SEMA3F 1.920649e+00 1.160158e+01 3.897990e+01 1.005768e+01 2.132158e+00 1.900993e+01
ANKIB1 1.860628e+01 2.384769e+01 2.471896e+01 2.246216e+01 7.817913e+00 2.104671e+01
CYP51A1 6.002027e+00 7.089854e+00 7.605835e+00 7.040379e+00 7.107194e+00 0.000000e+00
X143_Hip_non.sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X150_Hip_non.sclerotic_pellet X152_Hip_non.sclerotic_adipocyte
TSPAN6 8.379315e-01 3.511316e+00 4.013709e+00 1.096754e+00 0.000000e+00 9.875994e-02
TNMD 1.523512e-01 4.681755e-01 4.224957e-01 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 2.163387e+01 1.310891e+01 1.256925e+01 8.303995e+00 2.140436e+01 1.135739e+01
SCYL3 3.427902e+00 1.006577e+01 3.696837e+00 1.253433e+00 0.000000e+00 2.567758e+00
C1orf112 4.037306e+00 4.681755e-01 4.330581e+00 5.640450e+00 0.000000e+00 1.876439e+00
FGR 4.018262e+02 1.065099e+01 1.573797e+02 1.909919e+02 1.169007e+02 3.905956e+02
CFH 3.808780e-01 1.521570e+00 1.267487e+00 1.096754e+00 0.000000e+00 0.000000e+00
FUCA2 1.630158e+01 1.427935e+01 2.355414e+01 1.081086e+01 8.232445e+00 1.570283e+01
GCLC 7.061477e+01 3.686882e+01 6.590933e+01 7.003558e+01 1.070218e+01 9.362442e+01
NFYA 6.223546e+01 3.359159e+01 5.344571e+01 3.775968e+01 3.622276e+01 6.873692e+01
STPG1 2.361443e+00 1.346005e+01 4.964325e+00 5.953808e+00 4.116223e+00 4.049157e+00
NIPAL3 2.727086e+01 2.177016e+01 2.513849e+01 2.553870e+01 1.646489e+00 3.624490e+01
LAS1L 4.920943e+01 5.629811e+01 4.489017e+01 4.371349e+01 4.692494e+01 5.263905e+01
ENPP4 5.636994e+00 4.213580e+00 5.069949e+00 1.723471e+00 5.762712e+00 4.147917e+00
SEMA3F 4.113482e+00 3.019732e+01 2.154728e+01 1.519788e+01 3.704600e+01 7.011956e+00
ANKIB1 1.500659e+01 3.874152e+01 2.556099e+01 1.535456e+01 4.116223e+00 1.106111e+01
CYP51A1 1.180722e+01 5.852194e+00 7.182427e+00 6.423846e+00 4.116223e+00 3.654118e+00
X152_Hip_non.sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet
TSPAN6 6.608755e-01 2.662070e+00 3.699158e-01 3.549722e+00 4.308813e+00 0.000000e+00
TNMD 0.000000e+00 1.613376e-01 0.000000e+00 0.000000e+00 6.431063e-02 0.000000e+00
DPM1 1.483966e+01 1.000293e+01 1.590638e+01 7.473099e+00 1.028970e+01 1.191379e+01
SCYL3 4.205571e+00 3.952771e+00 3.847124e+00 3.736549e+00 4.566055e+00 2.037886e+00
C1orf112 3.905173e+00 1.936051e+00 2.145512e+00 1.681447e+00 4.308813e+00 4.075771e+00
FGR 2.370741e+02 1.414931e+02 3.505322e+02 1.393733e+02 2.176272e+02 4.213720e+02
CFH 6.007959e-02 1.452038e+00 1.553646e+00 7.473099e-01 4.308813e+00 0.000000e+00
FUCA2 1.315743e+01 2.073188e+01 1.472265e+01 8.780891e+00 2.083665e+01 2.069238e+01
GCLC 1.074223e+02 7.106921e+01 9.270090e+01 6.389499e+01 1.232835e+02 6.552586e+01
NFYA 5.052693e+01 4.017306e+01 5.238008e+01 3.867328e+01 4.456727e+01 3.636842e+01
STPG1 6.188198e+00 7.744205e+00 4.734922e+00 7.473099e-01 5.209161e+00 3.291969e+00
NIPAL3 2.853780e+01 3.025080e+01 3.107293e+01 3.045288e+01 2.418080e+01 2.414111e+01
LAS1L 7.119431e+01 4.670724e+01 6.051822e+01 5.679555e+01 5.222024e+01 6.286093e+01
ENPP4 2.823741e+00 4.840128e+00 1.701613e+00 2.428757e+00 3.344153e+00 2.978448e+00
SEMA3F 3.905173e+00 2.290994e+01 4.586956e+00 3.699184e+01 1.948612e+01 2.351406e+00
ANKIB1 1.910531e+01 2.484599e+01 1.709011e+01 2.858460e+01 2.353769e+01 1.724365e+01
CYP51A1 6.728914e+00 1.048694e+01 4.438989e+00 2.055102e+00 5.466404e+00 1.065971e+01
X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X79_Hip_non.sclerotic_pellet
TSPAN6 7.497589 3.230584e+00 3.869183e+00
TNMD 0.000000 0.000000e+00 0.000000e+00
DPM1 2.044797 1.102199e+01 1.702441e+01
SCYL3 6.815990 5.130928e+00 2.631045e+00
C1orf112 0.000000 5.701031e-01 4.643020e-01
FGR 36.806347 1.571584e+02 9.685339e+02
CFH 0.000000 3.990722e+00 6.190693e-01
FUCA2 0.681599 1.045189e+01 1.114325e+01
GCLC 65.433507 7.981444e+01 4.426346e+01
NFYA 5.452792 4.275773e+01 5.710914e+01
STPG1 0.000000 7.601375e+00 4.952554e+00
NIPAL3 10.905584 2.033368e+01 2.089359e+01
LAS1L 54.527922 3.382612e+01 5.323996e+01
ENPP4 0.000000 1.520275e+00 3.869183e+00
SEMA3F 62.707110 2.451443e+01 1.470290e+01
ANKIB1 14.995179 1.881340e+01 9.595574e+00
CYP51A1 12.268782 1.976357e+01 1.036941e+01
[ reached getOption("max.print") -- omitted 23208 rows ]
$bone_non_sclerotic_hip_vs_tibia$fit
An object of class "DGEGLM"
$coefficients
(Intercept) batchpellet grouptibia
TSPAN6 -12.76658 -0.4524918 1.3247510
TNMD -15.05776 -2.2775275 1.1007186
DPM1 -11.47353 0.2197903 0.2142905
SCYL3 -12.23994 -0.2014172 -0.1076753
C1orf112 -13.24306 0.8728437 -0.9187555
23220 more rows ...
$fitted.values
X102_tibia_non.sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte
TSPAN6 80.1935126 28.259036 21.2486082 14.873157 45.379388 23.341462
TNMD 0.7264813 2.343593 0.1924933 1.233468 3.763426 1.935766
DPM1 189.0640639 33.887326 50.0956759 17.835411 54.417500 27.990329
SCYL3 41.5938606 11.376114 11.0209868 5.987421 18.268178 9.396468
C1orf112 19.6973367 1.814149 5.2191378 0.954814 2.913227 1.498455
X128_tibia_non.sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte
TSPAN6 68.7940412 37.394734 54.2210293 146.056704 66.4429451 63.319388
TNMD 0.6232123 3.101239 0.4911939 12.112848 0.6019135 5.251235
DPM1 162.1886930 44.842560 127.8313896 175.146492 156.6457536 75.930569
SCYL3 35.6813122 15.053832 28.1227478 58.797397 34.4618724 25.490204
C1orf112 16.8973693 2.400635 13.3179086 9.376421 16.3198870 4.064923
X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte X151_Tibia_non.sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte
TSPAN6 141.928339 48.850168 12.3073169 23.104445 22.4095422 83.411354
TNMD 1.285744 4.051267 0.1114933 1.916109 0.2030104 6.917512
DPM1 334.609967 58.579547 29.0157056 27.706106 52.8326914 100.024208
SCYL3 73.613780 19.665395 6.3834194 9.301054 11.6231269 33.578537
C1orf112 34.860804 3.136041 3.0229548 1.483239 5.5042894 5.354770
X155_Tibia_non.sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte X159_Tibia_non.sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte
TSPAN6 22.9911699 81.761814 5.65439290 70.155596 81.262231 122.85424
TNMD 0.2082794 6.780712 0.05122373 5.818179 0.736163 10.18861
DPM1 54.2039358 98.046132 13.33078532 84.128329 191.583671 147.32285
SCYL3 11.9247989 32.914489 2.93275631 28.242226 42.148171 49.45689
C1orf112 5.6471503 5.248874 1.38884652 4.503788 19.959838 7.88689
X160_Tibia_non.sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_adipocyte
TSPAN6 17.1309020 146.397446 8.05383443 17.890662 12.7966010 23.265195
TNMD 0.1551906 12.141106 0.07296052 1.483717 0.1159257 1.929441
DPM1 40.3877800 175.555099 18.98770384 21.453905 30.1692406 27.898872
SCYL3 8.8852617 58.934568 4.17727140 7.202164 6.6371957 9.365766
C1orf112 4.2077362 9.398296 1.97820352 1.148529 3.1431340 1.493559
X164_tibia_non.sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6 31.5132316 30.630415 20.577086 14.132433 1.93889668 19.662850
TNMD 0.2854816 2.540257 0.186410 1.219199 0.01827143 1.696305
DPM1 74.2955313 36.731006 48.512497 51.796839 13.97110645 72.066395
SCYL3 16.3449251 12.330750 10.672690 24.014607 4.24489167 33.412196
C1orf112 7.7403610 1.966385 5.054197 8.725846 4.58034234 12.140514
X125_Hip_non.sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X143_Hip_non.sclerotic_adipocyte
TSPAN6 14.9584532 13.185022 1.88867700 8.4494312 2.52648330 4.1723587
TNMD 0.1409628 1.137466 0.01779818 0.7289286 0.02380863 0.3599475
DPM1 107.7861160 48.324478 13.60923854 30.9680462 18.20507896 15.2921295
SCYL3 32.7490444 22.404714 4.13494403 14.3577381 5.53131481 7.0899013
C1orf112 35.3370231 8.140882 4.46170614 5.2169671 5.96842450 2.5761566
X143_Hip_non.sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X150_Hip_non.sclerotic_pellet X152_Hip_non.sclerotic_adipocyte
TSPAN6 23.5721272 24.202236 26.818956 11.4604948 2.18115113 28.682921
TNMD 0.2221349 2.087916 2.313659 0.1079994 0.02055435 2.474463
DPM1 169.8536604 88.703716 98.294271 82.5808797 15.71671916 105.125897
SCYL3 51.6072503 41.125769 45.572245 25.0908466 4.77526747 48.739597
C1orf112 55.6854903 14.943286 16.558939 27.0736395 5.15263086 17.709814
X152_Hip_non.sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet
TSPAN6 29.8873665 35.115478 24.2706687 15.162244 44.047513 11.4545535
TNMD 0.2816473 3.029396 0.2287177 1.308040 3.799959 0.1079434
DPM1 215.3593764 128.701886 174.8871408 55.571203 161.438727 82.5380681
SCYL3 65.4334162 59.670151 53.1365908 25.764518 74.847956 25.0778390
C1orf112 70.6042627 21.681494 57.3356862 9.361687 27.196437 27.0596040
X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X79_Hip_non.sclerotic_pellet
TSPAN6 4.155997 9.44892586 11.6020659
TNMD 0.358536 0.08904313 0.1093335
DPM1 15.232162 68.08611853 83.6009980
SCYL3 7.062099 20.68685098 25.4007928
C1orf112 2.566054 22.32162016 27.4080791
23220 more rows ...
$deviance
[1] 90.06658 27.14808 21.87904 40.69051 54.05294
23220 more elements ...
$iter
[1] 7 6 3 4 6
23220 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
23220 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_non.sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte
TSPAN6 3 12 17 26 43 16
TNMD 0 0 1 10 4 0
DPM1 177 33 57 6 70 34
SCYL3 61 26 7 14 10 4
C1orf112 71 0 9 0 1 0
X128_tibia_non.sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte
TSPAN6 75 28 4 65 26 33
TNMD 0 0 0 1 0 3
DPM1 153 38 159 174 218 101
SCYL3 24 8 16 50 38 18
C1orf112 6 2 23 16 37 19
X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte X151_Tibia_non.sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte
TSPAN6 17 59 15 4 42 43
TNMD 0 13 0 0 0 0
DPM1 356 66 20 26 48 96
SCYL3 37 12 4 11 23 21
C1orf112 75 0 0 0 4 3
X155_Tibia_non.sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte X159_Tibia_non.sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte
TSPAN6 29 75 26 66 66 135
TNMD 0 12 0 8 5 12
DPM1 45 59 12 79 150 155
SCYL3 0 38 4 36 26 27
C1orf112 3 10 1 2 6 8
X160_Tibia_non.sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_adipocyte
TSPAN6 11 107 24 17 3 52
TNMD 0 13 0 0 0 0
DPM1 49 266 10 23 25 32
SCYL3 14 44 12 19 4 11
C1orf112 11 9 0 0 0 1
X164_tibia_non.sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_pellet X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X125_Hip_non.sclerotic_adipocyte
TSPAN6 65 4 31 30 4 35
TNMD 0 0 0 5 0 0
DPM1 54 25 84 67 18 91
SCYL3 16 0 6 30 10 13
C1orf112 6 0 0 6 7 25
X125_Hip_non.sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X143_Hip_non.sclerotic_adipocyte
TSPAN6 14 0 0 0 0 10
TNMD 0 2 0 0 0 0
DPM1 87 52 1 18 7 18
SCYL3 40 22 14 8 0 9
C1orf112 40 0 0 14 14 0
X143_Hip_non.sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X150_Hip_non.sclerotic_pellet X152_Hip_non.sclerotic_adipocyte
TSPAN6 11 30 38 7 0 1
TNMD 2 4 4 0 0 0
DPM1 284 112 119 53 26 115
SCYL3 45 86 35 8 0 26
C1orf112 53 4 41 36 0 19
X152_Hip_non.sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_non.sclerotic_pellet
TSPAN6 11 33 5 19 67 0
TNMD 0 2 0 0 1 0
DPM1 247 124 215 40 160 76
SCYL3 70 49 52 20 71 13
C1orf112 65 24 29 9 67 26
X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X79_Hip_non.sclerotic_pellet
TSPAN6 11 17 25
TNMD 0 0 0
DPM1 3 58 110
SCYL3 10 27 17
C1orf112 0 3 3
23220 more rows ...
$unshrunk.coefficients
(Intercept) batchpellet grouptibia
TSPAN6 -12.77427 -0.4558879 1.3318492
TNMD -15.22455 -2.6701447 1.2923996
DPM1 -11.47542 0.2201276 0.2146202
SCYL3 -12.24408 -0.2024806 -0.1082380
C1orf112 -13.25645 0.8859497 -0.9317646
23220 more rows ...
$df.residual
[1] 54 54 54 54 54
23220 more elements ...
$design
(Intercept) batchpellet grouptibia
X102_tibia_non.sclerotic_pellet 1 1 1
X104_tibia_non.sclerotic_adipocyte 1 0 1
X104_tibia_non.sclerotic_pellet 1 1 1
X105_tibia_non.sclerotic_adipocyte 1 0 1
X109_tibia_non.sclerotic_adipocyte 1 0 1
52 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 16.28275 14.78384 14.9546 14.14198 15.25748 14.59265 16.12943 15.06395 15.89138 16.42642 16.09465 15.59061 16.85363 15.33118 14.4085 14.58245 15.0078 15.86621 15.03342 15.84623 13.63074 15.69314 16.29599 16.25342
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 14.73919 16.42875 13.98446 14.3267 14.44749 14.58938 15.34872 14.86442 14.92249 15.42274 13.89228 15.753 15.93544 15.35335 13.86604 14.90837 14.15699 14.20275 16.39022 15.96072 16.06338 15.66907 14.01001 16.13057
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] 16.6276 16.33291 16.41943 15.49308 16.55954 15.66855 14.19882 15.47606 15.68134
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 57
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23220 more rows ...
$dispersion
[1] 0.5889180 4.8757760 0.3757245 0.7618057 1.3851652
23220 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 2.651109 -0.629285 3.758090 2.151322 1.138241
23220 more elements ...
$df.residual.zeros
[1] 54 54 54 54 54
23220 more elements ...
$df.prior
[1] 11.2477 11.2477 11.2477 11.2477 11.2477
23220 more elements ...
$var.post
[1] 1.5497571 0.5400086 0.4713473 0.8038724 1.0121531
23220 more elements ...
$var.prior
[1] 0.9825569 0.7189235 0.7890759 1.0455749 1.0657926
23220 more elements ...
$samples52 more rows ...
$genes23220 more rows ...
$bone_non_sclerotic_hip_vs_tibia$mds_plot
$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect
$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$w
[1] 0.8818924
$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$h
[1] 0.6859077
$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$left
[1] 2.970551
$bone_non_sclerotic_hip_vs_tibia$mds_plot$rect$top
[1] 1.886048
$bone_non_sclerotic_hip_vs_tibia$mds_plot$text
$bone_non_sclerotic_hip_vs_tibia$mds_plot$text$x
[1] 3.326605 3.326605
$bone_non_sclerotic_hip_vs_tibia$mds_plot$text$y
[1] 1.657412 1.428776
$bone_non_sclerotic_hip_vs_tibia$ql_disp_plot
NULL
$bone_non_sclerotic_hip_vs_tibia$boxplot_gg
$bone_sclerotic_hip_vs_tibia
$bone_sclerotic_hip_vs_tibia$name
[1] "tibia-vs-hip"
$bone_sclerotic_hip_vs_tibia$results
Coefficient: grouptibia
$bone_sclerotic_hip_vs_tibia$colsums_samples
$bone_sclerotic_hip_vs_tibia$normalized_matrix
X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X105_tibia_sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_sclerotic_adipocyte
TSPAN6 6.109276e+00 9.139053e+00 4.490814e+00 9.944566e+00 6.835935e+00 4.602659e+00
TNMD 0.000000e+00 0.000000e+00 1.496938e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.842723e+00 1.370858e+01 9.480608e+00 1.370140e+01 6.835935e+00 5.523191e+00
SCYL3 8.824510e+00 3.263947e+00 2.993876e+00 2.872875e+00 6.214486e+00 4.602659e+00
C1orf112 0.000000e+00 0.000000e+00 0.000000e+00 4.861788e+00 0.000000e+00 0.000000e+00
FGR 3.937089e+01 2.033439e+02 6.536630e+01 8.066148e+01 6.960224e+01 3.221861e+01
CFH 1.357617e+00 3.590342e+00 6.486732e+00 5.082778e+00 2.485794e+00 0.000000e+00
FUCA2 2.647353e+01 1.893090e+01 1.297346e+01 1.723725e+01 1.719341e+01 1.564904e+01
GCLC 2.579472e+01 1.958368e+01 8.981628e+00 3.469548e+01 1.035748e+01 3.590074e+01
NFYA 1.764902e+01 3.492424e+01 5.239283e+01 1.790022e+01 3.148673e+01 5.339084e+01
STPG1 1.086094e+01 6.201500e+00 5.488773e+00 6.187730e+00 8.285982e-01 2.761595e+00
NIPAL3 8.824510e+00 1.044463e+01 1.297346e+01 7.955653e+00 1.222182e+01 8.284786e+00
LAS1L 3.088579e+01 3.753540e+01 4.141529e+01 4.751293e+01 2.216500e+01 3.221861e+01
ENPP4 0.000000e+00 4.569526e+00 4.989794e-01 1.767923e+00 3.314393e+00 3.682127e+00
SEMA3F 4.072851e+01 2.252124e+01 3.293264e+01 2.497191e+01 5.178738e+01 2.025170e+01
ANKIB1 1.357617e+01 1.370858e+01 1.447040e+01 9.723575e+00 1.056463e+01 3.129808e+01
CYP51A1 1.663081e+01 8.159869e+00 1.147653e+01 1.679527e+01 8.700281e+00 1.196691e+01
X128_tibia_sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_sclerotic_adipocyte
TSPAN6 3.431038e+00 2.926414e+00 1.351337e+01 7.165749e+00 6.338898e+00 9.943108e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.016922e+00 0.000000e+00
DPM1 1.315231e+01 1.268113e+01 2.852823e+01 1.213554e+01 1.296593e+01 2.272710e+01
SCYL3 3.431038e+00 0.000000e+00 1.051040e+01 3.582875e+00 5.474503e+00 2.840888e+00
C1orf112 0.000000e+00 0.000000e+00 0.000000e+00 1.618072e+00 1.152527e+00 0.000000e+00
FGR 8.177308e+01 1.950942e+02 8.558469e+01 1.089887e+02 4.811800e+01 4.460194e+02
CFH 4.002878e+00 3.901885e+00 6.005943e+00 2.542685e+00 4.610108e+00 0.000000e+00
FUCA2 2.001439e+01 1.170565e+01 3.002972e+00 1.583399e+01 4.898240e+00 4.261332e+00
GCLC 5.146558e+00 2.536225e+01 2.852823e+01 2.958761e+01 7.203294e+00 1.193173e+02
NFYA 3.831326e+01 1.658301e+01 2.702674e+01 2.646704e+01 2.650812e+01 5.681776e+01
STPG1 1.543967e+01 0.000000e+00 1.351337e+01 1.849226e+00 1.728790e+00 8.522664e+00
NIPAL3 2.802015e+01 3.901885e+00 1.801783e+01 6.472290e+00 2.103362e+01 5.681776e+00
LAS1L 2.287359e+01 1.073018e+01 3.903863e+01 3.409510e+01 4.033844e+01 2.130666e+01
ENPP4 3.431038e+00 3.901885e+00 4.504457e+00 3.351721e+00 3.457581e+00 4.261332e+00
SEMA3F 3.145119e+01 1.463207e+01 1.951931e+01 1.421592e+01 3.515207e+01 1.704533e+01
ANKIB1 9.721275e+00 1.560754e+01 1.201189e+01 1.502496e+01 2.362680e+01 0.000000e+00
CYP51A1 1.029312e+01 2.926414e+00 0.000000e+00 1.109535e+01 9.508348e+00 1.420444e+00
X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_sclerotic_adipocyte X155_Tibia_sclerotic_pellet
TSPAN6 1.153695e+01 9.347641 0.000000e+00 4.696195e+01 7.279063e+00 3.728945e+00
TNMD 0.000000e+00 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.439323e+00 0.000000 2.626272e+01 4.696195e+00 1.273836e+01 1.193262e+01
SCYL3 7.341696e+00 1.335377 0.000000e+00 6.261594e+00 4.549414e-01 7.457889e-01
C1orf112 6.992091e-01 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
FGR 5.348950e+01 85.464149 1.505729e+02 3.130797e+01 5.277321e+01 8.576573e+01
CFH 4.544859e+00 26.707546 8.754239e+00 1.565398e+01 5.914239e+00 1.044105e+01
FUCA2 1.608181e+01 10.683019 1.400678e+01 0.000000e+00 2.593166e+01 5.220523e+00
GCLC 1.713062e+01 30.713678 2.276102e+01 1.252319e+01 9.553770e+00 1.416999e+01
NFYA 3.705808e+01 30.713678 0.000000e+00 3.287337e+01 2.866131e+01 1.118683e+01
STPG1 8.040905e+00 5.341509 0.000000e+00 6.261594e+00 2.729649e+00 2.237367e+00
NIPAL3 1.258576e+01 29.378301 1.750848e+01 2.504637e+01 7.279063e+00 2.983156e+01
LAS1L 2.726916e+01 41.396697 1.750848e+01 4.070036e+01 4.594909e+01 2.461104e+01
ENPP4 4.894464e+00 0.000000 0.000000e+00 4.696195e+00 6.369180e+00 1.491578e+00
SEMA3F 3.426125e+01 28.042924 2.451187e+01 1.721938e+01 1.410318e+01 3.505208e+01
ANKIB1 1.433379e+01 18.695283 1.400678e+01 1.408859e+01 7.734005e+00 9.695256e+00
CYP51A1 1.188656e+01 38.725942 4.377120e+01 0.000000e+00 1.637789e+01 1.118683e+01
X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_sclerotic_adipocyte X160_Tibia_sclerotic_pellet
TSPAN6 2.534194e+00 1.450756e+01 8.972121e+00 6.528036e+00 8.784107e+00 3.183674e+00
TNMD 0.000000e+00 0.000000e+00 1.451373e+00 0.000000e+00 3.331903e+00 0.000000e+00
DPM1 9.412721e+00 1.994789e+01 1.121515e+01 9.671165e+00 1.262084e+01 9.647496e+00
SCYL3 1.810139e+00 9.067223e-01 3.958289e-01 3.626687e+00 3.331903e+00 3.858998e+00
C1orf112 0.000000e+00 9.067223e-01 2.638859e-01 2.417791e-01 8.077339e-01 5.788497e-01
FGR 2.642802e+01 7.616467e+01 2.889551e+01 3.457441e+01 2.100108e+01 4.341373e+01
CFH 1.086083e+00 9.067223e-01 2.111087e+00 2.901349e+00 3.836736e+00 5.113173e+00
FUCA2 7.602582e+00 9.067223e+00 1.926367e+01 2.877171e+01 1.554888e+01 9.743971e+00
GCLC 2.679005e+01 1.722772e+01 4.301341e+01 1.885877e+01 3.382386e+01 2.672356e+01
NFYA 2.570397e+01 1.813445e+01 3.179825e+01 3.167306e+01 3.483353e+01 2.527644e+01
STPG1 1.448111e+00 6.347056e+00 5.937433e+00 9.671165e-01 8.279273e+00 2.411874e+00
NIPAL3 8.688666e+00 4.533611e+00 1.095127e+01 8.462269e+00 1.039957e+01 1.061225e+01
LAS1L 5.104591e+01 5.258989e+01 4.182592e+01 2.466147e+01 4.230507e+01 3.444156e+01
ENPP4 3.620277e+00 9.067223e-01 4.090232e+00 4.110245e+00 3.029002e+00 1.833024e+00
SEMA3F 3.258250e+01 1.994789e+01 1.886784e+01 4.956472e+01 2.736199e+01 7.139147e+01
ANKIB1 1.556719e+01 9.067223e+00 1.768036e+01 1.063828e+01 1.615468e+01 1.157699e+01
CYP51A1 1.520516e+01 1.722772e+01 2.731219e+01 1.910055e+01 1.726531e+01 1.292764e+01
X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_sclerotic_adipocyte
TSPAN6 6.647082e+00 1.557189e+01 1.989227e+00 5.762564e+00 7.098767e+00 4.784526e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.196132e+00
DPM1 8.459923e+00 9.966012e+00 3.315378e+00 9.220102e+00 3.042329e+01 1.510116e+01
SCYL3 2.296265e+00 2.491503e+00 3.978454e+00 4.840553e+00 1.014110e+00 2.990329e-01
C1orf112 1.087704e+00 1.245752e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.196132e+00
FGR 4.332689e+01 5.813507e+01 1.336098e+02 4.310398e+01 9.329808e+01 7.849614e+01
CFH 1.571129e+00 2.076253e-01 1.326151e+00 2.996533e+00 1.014110e+01 5.980658e+00
FUCA2 1.099790e+01 2.325403e+01 3.348532e+01 2.420277e+01 0.000000e+00 7.924372e+00
GCLC 2.652790e+01 1.744052e+01 2.055535e+01 1.797920e+01 1.419753e+01 4.036944e+01
NFYA 2.852203e+01 2.449978e+01 1.491920e+01 1.106412e+01 3.447972e+01 4.231316e+01
STPG1 4.229962e+00 7.474509e+00 6.630757e+00 8.067589e+00 9.126986e+00 1.046615e+01
NIPAL3 1.281074e+01 1.889390e+01 1.525074e+01 1.498267e+01 1.521164e+01 2.033424e+01
LAS1L 2.580277e+01 2.719891e+01 4.376300e+01 3.319237e+01 2.028219e+01 5.143366e+01
ENPP4 4.109106e+00 4.983006e+00 2.652303e+00 2.074523e+00 2.028219e+00 2.541780e+00
SEMA3F 3.251028e+01 3.965642e+01 2.685457e+01 3.895493e+01 2.332452e+01 4.620058e+01
ANKIB1 1.559043e+01 1.453377e+01 1.624535e+01 8.298092e+00 6.084657e+00 2.182940e+01
CYP51A1 1.335459e+01 1.598714e+01 1.027767e+01 2.374176e+01 1.825397e+01 1.480213e+01
X108_Hip_sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet
TSPAN6 3.625694e+00 1.124589e+00 8.251374e-01 6.962937e+00 0.000000e+00 2.702499e+00 2.277740e-01
TNMD 0.000000e+00 9.371572e-02 0.000000e+00 3.481468e-01 0.000000e+00 3.378123e-01 0.000000e+00
DPM1 2.406142e+01 4.779502e+00 1.746541e+01 6.614790e+00 5.863920e+00 7.094059e+00 1.488123e+01
SCYL3 3.296085e-01 1.874314e+00 5.225870e+00 3.829615e+00 5.863920e+00 1.351249e+00 3.568459e+00
C1orf112 0.000000e+00 1.499451e+00 4.400733e+00 0.000000e+00 7.818561e+00 1.013437e+00 1.366644e+00
FGR 2.472064e+02 5.429889e+02 4.620770e+02 3.481468e+01 6.938973e+01 3.979429e+02 3.439387e+02
CFH 3.296085e-01 1.968030e+00 1.100183e+00 0.000000e+00 2.931960e+00 0.000000e+00 2.277740e-01
FUCA2 1.318434e+01 1.883686e+01 8.526420e+00 1.984437e+01 1.221650e+01 1.705952e+01 1.313496e+01
GCLC 2.274299e+01 5.501113e+01 6.614852e+01 1.288143e+01 1.417114e+01 5.658357e+01 3.560866e+01
NFYA 4.812285e+01 4.779502e+01 4.717036e+01 4.247392e+01 2.492166e+01 3.614592e+01 5.375465e+01
STPG1 3.955302e+00 4.592070e+00 6.188531e+00 2.785175e+00 4.886600e-01 0.000000e+00 2.049966e+00
NIPAL3 2.109495e+01 1.246419e+01 1.347724e+01 9.748112e+00 1.661444e+01 1.283687e+01 3.401424e+01
LAS1L 5.735188e+01 4.385896e+01 4.428237e+01 4.874056e+01 4.251342e+01 5.303654e+01 4.851585e+01
ENPP4 1.087708e+01 1.499451e+00 4.400733e+00 2.785175e+00 9.773201e-01 2.026874e+00 6.377671e+00
SEMA3F 3.955302e+01 1.499451e+01 1.388981e+01 6.614790e+00 5.179796e+01 1.486374e+01 7.592465e+00
ANKIB1 1.483238e+01 2.155462e+01 1.499000e+01 2.506657e+01 3.176290e+01 2.094437e+01 1.457753e+01
CYP51A1 1.120669e+01 1.049616e+01 5.363393e+00 1.775549e+01 6.841241e+00 7.431872e+00 7.212842e+00
X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_sclerotic_adipocyte
TSPAN6 2.041447e+00 6.260208e-01 2.640983e+00 0.000000e+00 3.508769e+00 2.178249e+00 8.616814e+00
TNMD 2.551809e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 2.066966e+01 3.756125e+00 1.419529e+01 1.138498e+00 1.197109e+01 1.176255e+01 1.126814e+01
SCYL3 2.041447e+00 1.085103e+01 3.301229e-01 9.107981e+00 3.439970e+00 2.323466e+00 3.579292e+00
C1orf112 2.296628e+00 2.086736e-01 1.980737e+00 0.000000e+00 2.751976e+00 3.775632e+00 7.953982e-01
FGR 6.175379e+01 4.569952e+01 1.914713e+01 2.903169e+01 2.251116e+02 3.499720e+02 2.704354e+01
CFH 1.531086e+00 7.094902e+00 8.253073e+00 3.984742e+00 1.513587e+00 0.000000e+00 2.253628e+00
FUCA2 1.454531e+01 1.356378e+01 2.013750e+01 2.504695e+01 1.231509e+01 1.786164e+01 1.458230e+01
GCLC 2.245592e+01 3.130104e+01 1.551578e+01 1.935446e+01 7.939450e+01 7.231787e+01 2.717611e+01
NFYA 4.210485e+01 2.524950e+01 3.961475e+01 2.675469e+01 5.669070e+01 6.055533e+01 2.704354e+01
STPG1 2.296628e+00 1.460715e+00 1.188442e+01 2.846244e+00 3.577568e+00 2.033033e+00 2.651327e+00
NIPAL3 1.352459e+01 1.961532e+01 8.913319e+00 2.220070e+01 2.015822e+01 2.468682e+01 9.279646e+00
LAS1L 2.985617e+01 3.463982e+01 4.951844e+01 2.447770e+01 4.258682e+01 3.339982e+01 3.513009e+01
ENPP4 1.020724e+00 0.000000e+00 6.602458e-01 0.000000e+00 4.196763e+00 3.049549e+00 6.628319e+00
SEMA3F 1.862821e+01 2.566685e+01 2.244836e+01 4.895540e+01 2.132781e+01 8.422563e+00 1.816159e+01
ANKIB1 1.633158e+01 2.191073e+01 3.268217e+01 1.650822e+01 2.800135e+01 1.945903e+01 2.651327e+01
CYP51A1 9.696876e+00 1.418980e+01 9.243441e+00 1.081573e+01 8.118328e+00 8.132130e+00 8.219115e+00
X150_Hip_sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet
TSPAN6 2.307693e+00 1.364561e+00 7.489405e-01 2.983063e+00 9.696885e-01 0.000000e+00 0.000000e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 3.232295e-01 0.000000e+00 0.000000e+00
DPM1 9.230770e+00 7.060122e+00 8.737639e+00 1.161825e+01 1.147465e+01 5.557702e+00 8.567166e+00
SCYL3 1.153846e+01 5.280259e+00 5.492230e+00 4.239090e+00 4.040369e+00 4.631419e+00 0.000000e+00
C1orf112 7.692309e-01 3.263081e+00 4.743290e+00 2.904562e+00 1.454533e+00 1.389426e+00 0.000000e+00
FGR 2.692308e+01 3.851623e+02 2.436553e+02 9.844109e+01 3.372900e+02 1.227326e+02 1.670597e+02
CFH 2.307693e+01 5.339588e-01 1.747528e+00 3.532575e+00 2.262607e+00 0.000000e+00 1.070896e+01
FUCA2 2.307693e+01 1.993446e+01 1.173340e+01 1.334528e+01 1.098980e+01 9.725979e+00 9.638062e+00
GCLC 2.538462e+01 1.282688e+02 5.317477e+01 4.717950e+01 6.828224e+01 6.483986e+01 1.392164e+01
NFYA 6.230770e+01 5.968473e+01 4.343855e+01 3.838732e+01 4.129257e+01 4.862989e+01 2.998508e+01
STPG1 6.153847e+00 4.983615e+00 1.497881e+00 4.474595e+00 3.959562e+00 4.631419e-01 0.000000e+00
NIPAL3 2.538462e+01 3.441068e+01 3.470091e+01 1.860490e+01 2.311091e+01 3.010422e+01 5.247389e+01
LAS1L 4.384616e+01 6.615156e+01 4.318890e+01 5.196810e+01 6.779739e+01 4.214591e+01 6.318285e+01
ENPP4 3.076923e+00 6.229519e+00 4.992936e+00 4.710100e+00 1.212111e+00 0.000000e+00 0.000000e+00
SEMA3F 2.769231e+01 4.864958e+00 7.239758e+00 2.488503e+01 4.040369e+00 1.065226e+01 2.677239e+01
ANKIB1 3.000000e+01 2.343486e+01 1.123411e+01 2.143096e+01 2.060588e+01 1.482054e+01 2.141791e+00
CYP51A1 1.076923e+01 5.932875e+00 1.223269e+01 8.870688e+00 9.292849e+00 1.852567e+00 8.567166e+00
X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 1.565662e+00 0.000000e+00 1.129774e+01 7.711789e+00 8.733780e+00
TNMD 2.012994e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.252530e+01 8.845968e+00 1.435118e+01 8.945676e+00 2.074273e+01
SCYL3 6.933647e+00 3.159274e+00 8.549639e+00 4.627074e+00 1.091723e+00
C1orf112 6.709981e-01 8.424731e-01 2.290082e+00 9.254147e-01 1.910514e+00
FGR 1.538822e+02 3.609997e+02 3.496191e+01 1.218463e+02 4.148546e+01
CFH 0.000000e+00 1.684946e+00 2.595426e+00 8.328732e+00 8.187919e+00
FUCA2 1.252530e+01 1.663884e+01 1.480920e+01 1.357275e+01 2.592841e+01
GCLC 5.233785e+01 3.327769e+01 3.877872e+01 2.591161e+01 1.637584e+01
NFYA 4.518054e+01 4.802097e+01 3.938941e+01 3.393187e+01 1.937807e+01
STPG1 3.802322e+00 2.738038e+00 1.282446e+01 3.393187e+00 2.183445e+00
NIPAL3 1.118330e+01 1.706008e+01 1.007636e+01 5.552488e+00 2.974944e+01
LAS1L 3.914155e+01 3.559449e+01 4.519095e+01 3.763353e+01 3.493512e+01
ENPP4 8.051977e+00 3.159274e+00 3.053442e-01 2.159301e+00 8.187919e-01
SEMA3F 2.348493e+01 1.832379e+01 3.480924e+01 3.177257e+01 2.456376e+01
ANKIB1 2.460326e+01 8.635350e+00 3.908406e+01 2.128454e+01 1.528412e+01
CYP51A1 5.144319e+00 1.284772e+01 2.213746e+01 8.328732e+00 6.004474e+00
[ reached getOption("max.print") -- omitted 23174 rows ]
$bone_sclerotic_hip_vs_tibia$fit
An object of class "DGEGLM"
$coefficients
(Intercept) batchpellet grouptibia
TSPAN6 -12.72109 -0.03627021 1.04015184
TNMD -15.05383 -1.31704314 0.69421662
DPM1 -11.43371 0.05389351 0.09336044
SCYL3 -12.51405 0.24892662 -0.18079516
C1orf112 -13.04351 -0.22212393 -1.25611269
23186 more rows ...
$fitted.values
X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X105_tibia_sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet
TSPAN6 24.854438 24.8810264 16.905913 38.172262 39.203738 9.1639435 14.2015950
TNMD 1.730266 0.3899298 1.176922 2.657400 0.614392 0.6379570 0.2225642
DPM1 34.936814 38.3459782 23.763914 53.657107 60.419762 12.8813612 21.8871217
SCYL3 8.963097 11.9736155 6.096671 13.765819 18.866203 3.3047344 6.8343016
C1orf112 1.747284 1.4375199 1.188497 2.683535 2.265025 0.6442313 0.8205078
X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet
TSPAN6 8.6478223 5.40866684 72.987971 28.1851492 5.9387779 24.129265 6.08145438
TNMD 0.6020267 0.08476339 5.081130 0.4417112 0.4134339 1.679783 0.09530716
DPM1 12.1558719 8.33569394 102.596051 43.4382047 8.3478846 33.917470 9.37257625
SCYL3 3.1186089 2.60283864 26.321186 13.5636743 2.1416635 8.701583 2.92660741
C1orf112 0.6079477 0.31248977 5.131103 1.6284181 0.4175000 1.696303 0.35136057
X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_sclerotic_adipocyte X155_Tibia_sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_sclerotic_adipocyte
TSPAN6 4.8180666 5.18783980 18.542389 10.8891884 23.301257 8.9564761 63.934456
TNMD 0.3354145 0.08130264 1.290847 0.1706529 1.622140 0.1403638 4.450860
DPM1 6.7725490 7.99536115 26.064239 16.7821284 32.753576 13.8034835 89.869915
SCYL3 1.7375086 2.49656898 6.686823 5.2402563 8.402984 4.3101679 23.056274
C1orf112 0.3387133 0.29973132 1.303542 0.6291310 1.638094 0.5174671 4.494635
X159_Tibia_sclerotic_pellet X160_Tibia_sclerotic_adipocyte X160_Tibia_sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_sclerotic_pellet
TSPAN6 33.5886594 83.549307 84.177661 139.599164 39.1139136 25.444158 35.2318722
TNMD 0.5263938 5.816368 1.319213 9.718334 0.6129843 1.771320 0.5521458
DPM1 51.7659513 117.441668 129.732380 196.228541 60.2813266 35.765759 54.2984273
SCYL3 16.1640314 30.129853 40.509219 50.342755 18.8229759 9.175764 16.9548025
C1orf112 1.9406099 5.873572 4.863427 9.813914 2.2598356 1.788741 2.0355478
X99_Tibia_sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6 8.0080466 19.822691 8.6565215 31.625629 20.7475502 8.5131274 5.8389536
TNMD 0.1255003 1.705185 0.1676337 2.720496 0.4017768 0.7323153 0.1130715
DPM1 12.3417891 72.226589 34.5819973 115.232147 82.8845312 31.0187023 23.3260761
SCYL3 3.8537506 24.405990 14.2226357 38.937941 34.0881552 10.4814883 9.5933812
C1orf112 0.4626709 14.388414 5.1639239 22.955643 12.3766539 6.1793021 3.4831442
X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6 17.547129 37.5801968 11.6145763 13.6733324 8.9779243 5.0123307 43.079138
TNMD 1.509437 0.7277414 0.9991077 0.2647844 0.7722979 0.0970639 3.705749
DPM1 63.935279 150.1293867 42.3192403 54.6236899 32.7122508 20.0237945 156.964520
SCYL3 21.604285 61.7441367 14.3000380 22.4652392 11.0537530 8.2352425 53.039671
C1orf112 12.736684 22.4179281 8.4305065 8.1566306 6.5166776 2.9900341 31.269238
X146_Hip_sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet
TSPAN6 19.6483260 22.357242 3.70924191 49.955852 11.4291995 37.754848 35.3094403
TNMD 0.3804903 1.923212 0.07182956 4.297296 0.2213267 3.247743 0.6837681
DPM1 78.4932329 81.461559 14.81807604 182.020734 45.6585878 137.564765 141.0579259
SCYL3 32.2821335 27.526567 6.09427197 61.506383 18.7781363 46.484326 58.0132915
C1orf112 11.7209275 16.228132 2.21269514 36.260740 6.8179253 27.404572 21.0633409
X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 6.3993752 2.6643708 13.251089 13.5470825 19.41297 9.2496799 10.4541706
TNMD 0.5504863 0.0515956 1.139884 0.2623396 1.66994 0.1791203 0.2024453
DPM1 23.3169673 10.6439131 48.282091 54.1193332 70.73370 36.9516099 41.7634379
SCYL3 7.8790053 4.3775522 16.314937 22.2578110 23.90153 15.1971929 17.1761670
C1orf112 4.6450230 1.5893922 9.618379 8.0813181 14.09101 5.5177641 6.2362857
23186 more rows ...
$deviance
[1] 71.42430 29.81002 38.80787 39.25253 37.47377
23186 more elements ...
$iter
[1] 7 6 3 3 6
23186 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
23186 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X105_tibia_sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet
TSPAN6 18 28 9 45 33 5 6
TNMD 0 0 3 0 0 0 0
DPM1 29 42 19 62 33 6 23
SCYL3 26 10 6 13 30 5 6
C1orf112 0 0 0 22 0 0 0
X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet
TSPAN6 3 9 62 22 7 33 7
TNMD 0 0 0 7 0 0 0
DPM1 13 19 105 45 16 27 0
SCYL3 0 7 31 19 2 21 1
C1orf112 0 0 14 4 0 2 0
X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_sclerotic_adipocyte X155_Tibia_sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_sclerotic_adipocyte
TSPAN6 0 30 16 5 7 16 68
TNMD 0 0 0 0 0 0 11
DPM1 15 3 28 16 26 22 85
SCYL3 0 4 1 1 5 1 3
C1orf112 0 0 0 0 0 1 2
X159_Tibia_sclerotic_pellet X160_Tibia_sclerotic_adipocyte X160_Tibia_sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_sclerotic_pellet
TSPAN6 27 87 33 110 75 6 25
TNMD 0 33 0 0 0 0 0
DPM1 40 125 100 140 48 10 40
SCYL3 15 33 40 38 12 12 21
C1orf112 1 8 6 18 6 0 0
X99_Tibia_sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6 7 32 11 12 6 20 0
TNMD 0 8 0 1 0 1 0
DPM1 30 101 73 51 127 19 12
SCYL3 1 2 1 20 38 11 12
C1orf112 0 8 0 16 32 0 16
X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_sclerotic_adipocyte
TSPAN6 16 3 8 3 8 0 51
TNMD 2 0 1 0 0 0 0
DPM1 42 196 81 18 43 2 174
SCYL3 8 47 8 52 1 16 50
C1orf112 6 18 9 1 6 0 40
X146_Hip_sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet
TSPAN6 15 65 3 23 3 38 12
TNMD 0 0 0 0 0 0 4
DPM1 81 85 12 119 35 148 142
SCYL3 16 27 15 89 22 54 50
C1orf112 26 6 1 55 19 37 18
X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 0 0 7 0 74 25 32
TNMD 0 0 9 0 0 0 0
DPM1 12 8 56 42 94 29 76
SCYL3 10 0 31 15 56 15 4
C1orf112 3 0 3 4 15 3 7
23186 more rows ...
$unshrunk.coefficients
(Intercept) batchpellet grouptibia
TSPAN6 -12.72903 -0.03801510 1.04599440
TNMD -15.18219 -1.52914827 0.83438695
DPM1 -11.43605 0.05402422 0.09351826
SCYL3 -12.52103 0.25050538 -0.18192739
C1orf112 -13.04944 -0.23422729 -1.28857555
23186 more rows ...
$df.residual
[1] 53 53 53 53 53
23186 more elements ...
$design
(Intercept) batchpellet grouptibia
X102_tibia_sclerotic_adipocyte 1 0 1
X102_tibia_sclerotic_pellet 1 1 1
X105_tibia_sclerotic_adipocyte 1 0 1
X109_tibia_sclerotic_adipocyte 1 0 1
X109_tibia_sclerotic_pellet 1 1 1
51 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 14.89607 14.93516 14.5107 15.32515 15.38982 13.89831 14.37441 13.84035 13.40906 15.97333 15.05985 13.46454 14.86646 13.5263 13.25541 13.36737 14.6031 14.10882 14.83155 13.91343 15.8409 15.23524 16.10847 16.15398
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 16.62181 15.38753 14.91952 15.283 13.8015 15.71586 14.92536 16.183 15.79948 14.87064 14.5316 15.59392 16.39352 15.18129 15.38249 14.9238 14.37895 16.49207 15.74504 15.83618 14.07787 16.64017 15.20322 16.36015 16.3312
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 14.58523 13.74702 15.31311 15.37322 15.69497 14.99164 15.11405
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 56
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23186 more rows ...
$dispersion
[1] 0.6676478 6.3532610 0.4097687 0.8868782 2.2707671
23186 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 2.5764710 -0.5620076 3.5953853 2.0772338 0.7359507
23186 more elements ...
$df.residual.zeros
[1] 53 53 53 53 53
23186 more elements ...
$df.prior
[1] 17.87419 17.87419 17.87419 17.87419 17.87419
23186 more elements ...
$var.post
[1] 1.2728244 0.5708394 0.7734800 0.8288521 0.7752235
23186 more elements ...
$var.prior
[1] 1.0510181 0.5957056 0.8958111 1.0904938 0.9773630
23186 more elements ...
$samples51 more rows ...
$genes23186 more rows ...
$bone_sclerotic_hip_vs_tibia$mds_plot
$bone_sclerotic_hip_vs_tibia$mds_plot$rect
$bone_sclerotic_hip_vs_tibia$mds_plot$rect$w
[1] 0.8358968
$bone_sclerotic_hip_vs_tibia$mds_plot$rect$h
[1] 0.7806285
$bone_sclerotic_hip_vs_tibia$mds_plot$rect$left
[1] 3.299757
$bone_sclerotic_hip_vs_tibia$mds_plot$rect$top
[1] 2.167356
$bone_sclerotic_hip_vs_tibia$mds_plot$text
$bone_sclerotic_hip_vs_tibia$mds_plot$text$x
[1] 3.637241 3.637241
$bone_sclerotic_hip_vs_tibia$mds_plot$text$y
[1] 1.907147 1.646937
$bone_sclerotic_hip_vs_tibia$ql_disp_plot
NULL
$bone_sclerotic_hip_vs_tibia$boxplot_gg
$hip_adipocytes_sclerotic_vs_non_sclerotic
$hip_adipocytes_sclerotic_vs_non_sclerotic$name
[1] "HSA-vs-HNSA"
$hip_adipocytes_sclerotic_vs_non_sclerotic$results
Coefficient: groupHSA
$hip_adipocytes_sclerotic_vs_non_sclerotic$colsums_samples
$hip_adipocytes_sclerotic_vs_non_sclerotic$normalized_matrix
X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte
TSPAN6 5.915820e+00 4.898332e+00 4.952515e+00 1.214547e+00 0.000000e+00 7.319304e+00
TNMD 9.859699e-01 1.224583e+00 0.000000e+00 1.012123e-01 4.238497e-01 3.659652e-01
DPM1 1.321200e+01 1.546036e+01 1.287654e+01 5.161827e+00 1.102009e+01 6.953338e+00
SCYL3 5.915820e+00 3.061457e-01 1.839506e+00 2.024246e+00 4.662346e+00 4.025617e+00
C1orf112 1.183164e+00 1.224583e+00 3.537511e+00 1.619397e+00 0.000000e+00 0.000000e+00
FGR 9.090643e+01 8.036326e+01 1.422079e+02 5.864240e+02 9.621387e+01 3.659652e+01
CFH 5.915820e+00 6.122915e+00 1.415004e+00 2.125458e+00 1.907323e+00 0.000000e+00
FUCA2 1.557833e+01 8.112862e+00 1.613105e+01 2.034367e+01 2.225211e+01 2.086002e+01
GCLC 3.865002e+01 4.132967e+01 6.056219e+01 5.941161e+01 2.309981e+01 1.354071e+01
NFYA 3.214262e+01 4.331962e+01 3.806362e+01 5.161827e+01 4.068957e+01 4.464775e+01
STPG1 1.163445e+01 1.071510e+01 3.820512e+00 4.959402e+00 2.331173e+00 2.927721e+00
NIPAL3 7.690566e+00 2.081791e+01 1.839506e+01 1.346123e+01 1.271549e+01 1.024703e+01
LAS1L 6.231330e+01 5.265707e+01 6.296770e+01 4.736735e+01 4.111342e+01 5.123513e+01
ENPP4 3.155104e+00 2.602239e+00 8.490026e-01 1.619397e+00 5.933895e+00 2.927721e+00
SEMA3F 5.521432e+01 4.729952e+01 2.603608e+01 1.619397e+01 1.144394e+01 6.953338e+00
ANKIB1 2.760716e+01 2.234864e+01 2.957359e+01 2.327883e+01 2.352366e+01 2.634949e+01
CYP51A1 1.005689e+01 1.515421e+01 1.160304e+01 1.133578e+01 6.993519e+00 1.866422e+01
KRIT1 1.045128e+01 8.878226e+00 9.056028e+00 1.639639e+01 1.059624e+01 1.756633e+01
RAD52 7.296178e+00 1.071510e+01 1.415004e+01 5.667888e+00 8.053143e+00 1.390668e+01
MYH16 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 4.238497e-01 0.000000e+00
BAD 3.470614e+01 2.816541e+01 2.518708e+01 3.906794e+01 3.751069e+01 6.148215e+01
LAP3 5.639748e+01 5.235092e+01 5.362867e+01 6.052495e+01 9.324692e+01 6.550777e+01
CD99 2.354496e+02 2.015970e+02 1.995156e+02 1.851173e+02 2.602437e+02 2.898444e+02
HS3ST1 7.887760e+00 9.490518e+00 7.075022e+00 1.143699e+01 2.161633e+01 2.561756e+01
AOC1 0.000000e+00 0.000000e+00 0.000000e+00 5.060614e+00 6.357745e-01 0.000000e+00
WNT16 0.000000e+00 1.683802e+00 0.000000e+00 4.048491e-01 0.000000e+00 0.000000e+00
HECW1 1.143725e+01 9.796664e+00 1.415004e-01 1.214547e+00 1.483474e+00 5.489478e+00
MAD1L1 6.310208e+00 4.898332e+00 5.943019e+00 1.002002e+01 5.298121e+00 8.783164e+00
LASP1 1.942361e+02 2.037400e+02 2.269667e+02 3.064708e+02 3.115295e+02 3.125343e+02
SNX11 7.887760e+00 1.239890e+01 1.372554e+01 1.416972e+01 2.882178e+01 1.280878e+01
TMEM176A 1.557833e+01 1.898104e+01 2.759259e+01 2.145700e+01 1.036312e+02 2.232388e+01
M6PR 3.786125e+01 4.500342e+01 4.386514e+01 6.730617e+01 7.586909e+01 3.989020e+01
KLHL13 0.000000e+00 0.000000e+00 1.698005e+00 1.012123e+00 4.238497e-01 1.097896e+00
CYP26B1 4.377707e+01 6.474982e+01 1.018803e+01 1.022244e+01 1.398704e+01 2.525160e+01
ICA1 1.163445e+01 1.683802e+00 7.782524e+00 7.995771e+00 7.205444e+00 9.515095e+00
DBNDD1 1.774746e+00 1.836874e+00 5.660018e-01 1.619397e+00 0.000000e+00 0.000000e+00
ALS2 1.183164e+01 1.836874e+01 2.858309e+01 1.578912e+01 1.949708e+01 2.232388e+01
CASP10 1.064848e+01 7.806716e+00 1.556505e+01 1.265154e+01 2.013286e+01 4.391582e+00
CFLAR 3.797956e+02 3.805392e+02 2.907834e+02 5.239760e+02 5.285405e+02 2.404391e+02
TFPI 7.355336e+01 7.240347e+01 2.363057e+01 1.892670e+01 2.119248e+01 9.515095e+00
X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6 0.000000e+00 2.870905e+00 6.763583e+00 2.117607e+00 3.357784e+00 2.714408e+00
TNMD 0.000000e+00 3.588631e-01 0.000000e+00 2.647009e-01 4.477046e-01 0.000000e+00
DPM1 6.165945e+00 7.536126e+00 1.217445e+01 2.144077e+01 1.253573e+01 1.458994e+01
SCYL3 2.740420e+00 1.435452e+00 6.087225e+00 2.117607e+00 9.625648e+00 3.393010e-01
C1orf112 4.795735e+00 1.076589e+00 0.000000e+00 2.382308e+00 4.477046e-01 2.035806e+00
FGR 4.528544e+02 4.227408e+02 2.110238e+02 6.405762e+01 1.018528e+01 1.967946e+01
CFH 0.000000e+00 0.000000e+00 0.000000e+00 1.588205e+00 1.455040e+00 8.482526e+00
FUCA2 9.591470e+00 1.812259e+01 2.502526e+01 1.508795e+01 1.365499e+01 2.069736e+01
GCLC 5.549351e+01 6.010957e+01 4.937416e+01 2.329368e+01 3.525673e+01 1.594715e+01
NFYA 2.980207e+01 3.839835e+01 2.637797e+01 4.367565e+01 3.212280e+01 4.071613e+01
STPG1 4.795735e+00 0.000000e+00 9.469017e+00 2.382308e+00 1.287151e+01 1.221484e+01
NIPAL3 2.021060e+01 1.363680e+01 1.826167e+01 1.402915e+01 2.081826e+01 9.161128e+00
LAS1L 6.268711e+01 5.634151e+01 3.584699e+01 3.097001e+01 5.383647e+01 5.089516e+01
ENPP4 0.000000e+00 2.153179e+00 1.555624e+01 1.058804e+00 4.029341e+00 6.786021e-01
SEMA3F 1.027658e+01 1.578998e+01 1.893803e+01 1.932317e+01 2.887694e+01 2.307247e+01
ANKIB1 2.295102e+01 2.224951e+01 2.096711e+01 1.694086e+01 3.704755e+01 3.359080e+01
CYP51A1 7.193603e+00 7.894989e+00 0.000000e+00 1.005863e+01 5.596307e+00 9.500429e+00
KRIT1 1.130423e+01 1.471339e+01 6.087225e+00 7.146925e+00 1.231188e+01 7.464623e+00
RAD52 2.432123e+01 1.991690e+01 1.014537e+01 1.561735e+01 9.961427e+00 6.446720e+00
MYH16 1.027658e+00 0.000000e+00 0.000000e+00 2.117607e+00 0.000000e+00 6.786021e-01
BAD 2.671910e+01 3.498915e+01 2.367254e+01 4.473445e+01 5.014291e+01 4.444844e+01
LAP3 4.967011e+01 7.446410e+01 4.058150e+01 3.917573e+01 4.499431e+01 7.532483e+01
CD99 8.084239e+01 2.739920e+02 1.170100e+02 2.514659e+02 2.369476e+02 2.392072e+02
HS3ST1 6.508498e+00 1.202191e+01 4.058150e+00 1.270564e+01 5.596307e+00 2.375107e+00
AOC1 0.000000e+00 3.588631e-01 1.826167e+01 1.852906e+00 5.596307e-01 1.017903e+00
WNT16 6.851050e-01 0.000000e+00 0.000000e+00 2.117607e+00 0.000000e+00 0.000000e+00
HECW1 3.768078e+00 1.256021e+00 0.000000e+00 7.941027e-01 3.022006e+00 2.035806e+00
MAD1L1 7.193603e+00 1.812259e+01 3.381792e+00 3.970514e+00 5.596307e+00 2.375107e+00
LASP1 3.216568e+02 4.137692e+02 2.117002e+02 2.496130e+02 2.989547e+02 2.558330e+02
SNX11 1.335955e+01 2.171122e+01 1.961439e+01 2.408778e+01 1.320728e+01 1.832226e+01
TMEM176A 1.781273e+01 2.906791e+01 2.029075e+01 1.283799e+02 1.298343e+01 6.107419e+01
M6PR 3.357015e+01 5.257345e+01 2.231982e+01 5.055787e+01 4.074112e+01 4.309123e+01
KLHL13 0.000000e+00 1.614884e+00 0.000000e+00 0.000000e+00 1.343114e+00 0.000000e+00
CYP26B1 1.986805e+01 7.715557e+00 9.469017e+00 4.155804e+01 2.786961e+01 1.832226e+01
ICA1 3.768078e+00 5.024084e+00 1.149809e+01 7.941027e+00 1.645314e+01 9.500429e+00
DBNDD1 7.193603e+00 0.000000e+00 0.000000e+00 0.000000e+00 3.245858e+00 3.053709e+00
ALS2 2.363612e+01 1.345737e+01 2.637797e+01 2.541129e+01 2.316871e+01 1.934016e+01
CASP10 2.363612e+01 7.536126e+00 4.261057e+01 1.614676e+01 1.477425e+01 1.119693e+01
CFLAR 4.932756e+02 7.227503e+02 1.907330e+02 2.226135e+02 2.422082e+02 1.720256e+02
TFPI 8.221260e+00 1.327794e+01 1.014537e+01 2.223488e+01 1.455040e+01 1.051833e+01
X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte
TSPAN6 3.854178e+00 3.598384e+00 8.695853e+00 9.697328e-02 1.318352e+00 2.599099e+00
TNMD 4.057030e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.575211e-01
DPM1 1.206966e+01 1.227684e+01 1.137150e+01 1.115193e+01 6.821039e+00 9.766310e+00
SCYL3 3.549901e+00 3.527827e+00 3.612124e+00 2.521305e+00 5.101449e+00 3.859268e+00
C1orf112 4.158455e+00 2.822262e+00 8.026942e-01 1.842492e+00 3.152581e+00 1.890254e+00
FGR 1.511244e+02 2.308610e+02 2.729160e+01 3.835293e+02 3.721192e+02 1.381460e+02
CFH 1.217109e+00 1.552244e+00 2.274300e+00 0.000000e+00 5.158769e-01 1.417690e+00
FUCA2 2.261794e+01 1.262962e+01 1.471606e+01 1.541875e+01 1.925940e+01 2.024146e+01
GCLC 6.328966e+01 8.142225e+01 2.742538e+01 9.193067e+01 1.239251e+02 6.938806e+01
NFYA 5.132142e+01 5.813859e+01 2.729160e+01 6.749340e+01 5.766357e+01 3.922276e+01
STPG1 4.767010e+00 3.668940e+00 2.675647e+00 3.975904e+00 4.814851e+00 7.561014e+00
NIPAL3 2.413933e+01 2.067307e+01 9.364765e+00 3.558919e+01 3.324540e+01 2.953521e+01
LAS1L 4.310594e+01 4.367450e+01 3.545233e+01 5.168676e+01 6.391141e+01 4.560237e+01
ENPP4 4.868436e+00 4.303949e+00 6.689118e+00 4.072878e+00 6.018563e+00 4.725634e+00
SEMA3F 2.069085e+01 2.187253e+01 1.832818e+01 6.885103e+00 4.700211e+00 2.236800e+01
ANKIB1 2.454503e+01 2.871651e+01 2.675647e+01 1.086101e+01 2.264126e+01 2.425825e+01
CYP51A1 6.896950e+00 8.325672e+00 8.294506e+00 3.588011e+00 5.731965e+00 1.023887e+01
KRIT1 1.318535e+01 7.902333e+00 1.551875e+01 1.037614e+01 1.180785e+01 7.167211e+00
RAD52 1.369247e+01 9.242907e+00 1.324445e+01 1.086101e+01 8.311349e+00 8.112338e+00
MYH16 0.000000e+00 0.000000e+00 8.026942e-01 4.848664e-01 0.000000e+00 0.000000e+00
BAD 2.444360e+01 3.160933e+01 5.551968e+01 3.277697e+01 2.447549e+01 5.150941e+01
LAP3 4.280166e+01 3.633662e+01 6.261014e+01 2.889804e+01 2.997818e+01 4.946163e+01
CD99 1.530514e+02 1.219923e+02 2.959266e+02 5.818397e+01 6.442729e+01 1.819369e+02
HS3ST1 6.694099e+00 6.208976e+00 8.160724e+00 3.781958e+00 4.700211e+00 6.222084e+00
AOC1 0.000000e+00 3.175045e+00 8.026942e-01 2.424332e+00 4.470933e+00 6.615887e+00
WNT16 2.028515e+00 0.000000e+00 1.070259e+00 9.697328e-01 1.146393e-01 0.000000e+00
HECW1 2.332792e+00 2.822262e-01 3.076994e+00 0.000000e+00 6.878358e-01 9.451268e-01
MAD1L1 5.071287e+00 1.086571e+01 9.364765e+00 1.270350e+01 9.572382e+00 5.040676e+00
LASP1 2.753709e+02 2.844840e+02 3.089035e+02 3.184602e+02 2.932473e+02 2.658169e+02
SNX11 1.612669e+01 1.467576e+01 2.033492e+01 2.812225e+01 2.413157e+01 2.205296e+01
TMEM176A 4.685869e+01 4.219281e+01 7.197491e+01 7.660889e+00 9.457743e+00 5.930670e+01
M6PR 4.655441e+01 5.877360e+01 4.441574e+01 7.224509e+01 6.351017e+01 5.938546e+01
KLHL13 7.099802e-01 7.761220e-01 2.408082e+00 4.848664e-01 4.585572e-01 2.205296e+00
CYP26B1 3.448475e+00 6.561759e+00 5.618859e+01 1.357626e+00 7.451555e-01 3.938028e+00
ICA1 1.135968e+01 8.043446e+00 8.160724e+00 1.173377e+01 1.197981e+01 1.173532e+01
DBNDD1 5.476990e+00 1.199461e+00 3.344559e+00 1.454599e+00 1.375672e+00 8.663662e-01
ALS2 1.906804e+01 1.912082e+01 1.806062e+01 1.968558e+01 2.189611e+01 1.677600e+01
CASP10 3.641184e+01 2.659982e+01 1.859575e+01 4.208640e+01 3.078065e+01 2.347065e+01
CFLAR 2.517387e+02 2.868829e+02 2.382664e+02 2.551367e+02 2.732428e+02 2.041474e+02
TFPI 3.154341e+01 2.250754e+01 1.150528e+01 7.079049e+00 8.139391e+00 1.653972e+01
X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte
TSPAN6 3.118367e+00 3.456795e+00 0.000000e+00 4.126355e+00 1.673259e+00 7.312985e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 6.158739e-02 2.151333e+00 0.000000e+00
DPM1 1.214522e+01 7.277462e+00 5.978896e+00 9.853982e+00 1.338607e+01 1.994451e+00
SCYL3 4.431363e+00 3.638731e+00 4.982413e+00 4.372705e+00 7.410146e+00 6.648168e+00
C1orf112 3.036305e+00 1.637429e+00 1.494724e+00 4.126355e+00 7.171109e-01 0.000000e+00
FGR 1.029061e+02 1.357247e+02 1.320339e+02 2.084117e+02 1.644574e+02 3.590011e+01
CFH 3.692803e+00 7.277462e-01 0.000000e+00 4.126355e+00 0.000000e+00 0.000000e+00
FUCA2 1.395059e+01 8.551018e+00 1.046307e+01 1.995431e+01 1.338607e+01 6.648168e-01
GCLC 4.931943e+01 6.222230e+01 6.975378e+01 1.180630e+02 5.593465e+01 6.382242e+01
NFYA 4.012846e+01 3.766087e+01 5.231534e+01 4.268006e+01 4.828547e+01 5.318535e+00
STPG1 4.677550e+00 7.277462e-01 4.982413e-01 4.988579e+00 4.063628e+00 0.000000e+00
NIPAL3 1.944876e+01 2.965566e+01 3.238569e+01 2.315686e+01 1.195185e+01 1.063707e+01
LAS1L 5.432523e+01 5.530871e+01 4.533996e+01 5.000896e+01 4.183147e+01 5.318535e+01
ENPP4 4.923737e+00 2.365175e+00 0.000000e+00 3.202544e+00 8.605331e+00 0.000000e+00
SEMA3F 2.601374e+01 3.602344e+01 1.145955e+01 1.866098e+01 2.509888e+01 6.116315e+01
ANKIB1 2.240300e+01 2.783629e+01 1.594372e+01 2.254098e+01 2.629407e+01 1.462597e+01
CYP51A1 9.273038e+00 2.001302e+00 1.992965e+00 5.234928e+00 5.497850e+00 1.196670e+01
KRIT1 5.580235e+00 9.824574e+00 9.964826e+00 1.040827e+01 1.147377e+01 8.642619e+00
RAD52 1.066810e+01 7.459399e+00 3.985930e+00 1.281018e+01 4.302665e+00 1.130189e+01
MYH16 2.461869e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
BAD 3.725628e+01 3.529569e+01 2.341734e+01 3.085528e+01 3.083577e+01 2.725749e+01
LAP3 4.259033e+01 5.712808e+01 5.530479e+01 4.169466e+01 6.119346e+01 1.861487e+01
CD99 1.816038e+02 1.530086e+02 1.609319e+02 1.299494e+02 1.565692e+02 3.231010e+02
HS3ST1 3.774865e+00 2.365175e+00 2.491207e+00 1.108573e+00 5.736887e+00 0.000000e+00
AOC1 1.477121e+00 7.459399e+00 6.477137e+00 3.140957e+00 1.673259e+00 0.000000e+00
WNT16 7.385606e-01 1.819366e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
HECW1 2.708055e+00 1.091619e+00 2.989448e+00 1.108573e+00 0.000000e+00 0.000000e+00
MAD1L1 7.057357e+00 1.473686e+01 3.487689e+00 8.252710e+00 1.912296e+00 3.124639e+01
LASP1 2.670307e+02 3.080186e+02 2.795134e+02 2.370499e+02 2.968839e+02 1.715227e+02
SNX11 8.944789e+00 2.747242e+01 2.541031e+01 1.724447e+01 1.721066e+01 5.983352e+00
TMEM176A 4.579076e+01 2.674467e+01 1.494724e+01 5.130230e+01 5.928117e+01 1.728524e+01
M6PR 5.933103e+01 3.966217e+01 4.683468e+01 6.682232e+01 5.784695e+01 1.529079e+01
KLHL13 2.790118e+00 2.910985e+00 0.000000e+00 2.648258e+00 1.195185e+00 0.000000e+00
CYP26B1 6.400858e+00 8.914891e+00 9.964826e+00 1.348764e+01 1.816681e+01 3.855938e+01
ICA1 5.005799e+00 8.187145e+00 4.982413e-01 9.915570e+00 1.864488e+01 2.659267e+00
DBNDD1 1.641246e+00 3.638731e-01 4.982413e-01 6.158739e-01 0.000000e+00 0.000000e+00
ALS2 1.731514e+01 1.455492e+01 1.444900e+01 2.352638e+01 1.266896e+01 5.318535e+00
CASP10 3.085542e+01 2.747242e+01 3.288393e+01 2.494289e+01 1.744970e+01 3.988901e+00
CFLAR 2.685899e+02 3.198445e+02 3.771687e+02 3.003001e+02 3.093138e+02 3.217714e+02
TFPI 2.289538e+01 1.655623e+01 8.968344e+00 2.420384e+01 2.246947e+01 1.329634e+00
X158_Hip_sclerotic_adipocyte
TSPAN6 1.170541e+01
TNMD 0.000000e+00
DPM1 1.486904e+01
SCYL3 8.858149e+00
C1orf112 2.372718e+00
FGR 3.622350e+01
CFH 2.689081e+00
FUCA2 1.534358e+01
GCLC 4.017803e+01
NFYA 4.081076e+01
STPG1 1.328722e+01
NIPAL3 1.043996e+01
LAS1L 4.682164e+01
ENPP4 3.163625e-01
SEMA3F 3.606532e+01
ANKIB1 4.049439e+01
CYP51A1 2.293628e+01
KRIT1 1.233814e+01
RAD52 8.383605e+00
MYH16 1.107269e+00
BAD 1.692539e+01
LAP3 8.462696e+01
CD99 2.741281e+02
HS3ST1 3.638168e+00
AOC1 1.581812e-01
WNT16 1.423631e+00
HECW1 1.739993e+00
MAD1L1 6.801793e+00
LASP1 2.303119e+02
SNX11 1.028178e+01
TMEM176A 8.288696e+01
M6PR 4.444892e+01
KLHL13 6.327249e-01
CYP26B1 2.878898e+01
ICA1 6.327249e+00
DBNDD1 4.745437e-01
ALS2 2.167083e+01
CASP10 1.154723e+01
CFLAR 2.560954e+02
TFPI 3.685623e+01
[ reached getOption("max.print") -- omitted 21583 rows ]
$hip_adipocytes_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 groupHSA
TSPAN6 -12.15943 -0.5473984 -0.4598270 -1.2795340 -0.2222066 -0.56536356 -0.3725572 0.4329859 -2.0090604 -0.6402360 -1.0044140 -0.58670075 0.56115060 0.07575426
TNMD -13.75752 -2.7835830 -0.9877961 -1.6904182 -1.8703239 -1.39395901 -1.6016356 -4.2275126 -4.1825180 -2.4168712 -4.1527976 -0.06935854 -4.20411251 0.10752944
DPM1 -11.19366 -0.4478492 -0.4475518 -0.7353736 0.1623264 -0.05665869 -0.1610301 -0.2694277 -0.4567248 -0.2700309 -0.7532161 -0.21623167 -0.48227961 0.08019759
SCYL3 -12.65366 -0.3197865 0.4627620 -0.3045499 0.3236600 0.51192455 0.2736772 0.4375748 0.4001212 0.4405716 0.4688902 0.80682697 1.08954615 -0.31037889
C1orf112 -13.68441 0.7768264 -4.2462710 0.9060191 0.0522886 -0.05655976 1.0689917 -0.4666419 0.7090236 0.6955757 0.2736322 0.76285920 0.07292938 0.13698081
21618 more rows ...
$fitted.values
X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte
TSPAN6 26.441999 36.871075 21.2825584 32.2065693 1.547709e+01 9.701243e+00
TNMD 5.284546 7.598621 0.3520143 0.5493088 1.783334e+00 1.152674e+00
DPM1 69.698907 97.292244 62.0255497 93.9619428 4.142678e+01 2.599442e+01
SCYL3 16.107646 15.181954 16.2801150 16.6526051 2.388391e+01 1.011923e+01
C1orf112 5.687384 8.440004 17.3838927 27.9966617 1.256013e-07 8.378591e-08
X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6 4.1958780 8.670562 6.1706255 17.0665864 26.407811 9.4291988
TNMD 0.5251942 1.119128 0.2191603 0.6250502 2.210797 0.8140047
DPM1 19.2069789 39.732343 23.9067648 66.1910112 116.024601 41.4718313
SCYL3 6.8265325 9.535174 6.5051807 12.1613258 47.478641 11.4589482
C1orf112 8.1809948 17.991571 1.7476155 5.1440116 9.443718 3.5885914
X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte
TSPAN6 35.365255 55.028002 6.500000e+01 7.059030e+00 1.292676e+01 34.7909482
TNMD 1.940472 3.113508 3.164652e-08 4.228408e-08 7.984672e-08 0.9912198
DPM1 115.331055 179.644509 8.500000e+01 8.970438e+01 1.644444e+02 133.1604158
SCYL3 41.276692 43.412612 2.700000e+01 4.903510e+01 6.069540e+01 62.8604307
C1orf112 32.524353 53.858493 6.000000e+00 2.365971e+01 4.610973e+01 28.7410358
X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte
TSPAN6 36.143278 1.045605e+01 4.132796e+00 46.99817 13.107014 1.375748e+01
TNMD 1.061859 2.227037e-08 9.076937e-09 15.74840 4.528922 6.400858e-09
DPM1 138.483219 3.552243e+01 1.405529e+01 179.71728 50.173380 1.275515e+01
SCYL3 44.141055 2.799564e+01 7.479468e+00 116.10763 21.887070 1.428007e+01
C1orf112 31.776223 8.135061e+00 3.421966e+00 39.41571 11.698515 1.815832e+00
X158_Hip_sclerotic_adipocyte
TSPAN6 6.258668e+01
TNMD 3.002735e-08
DPM1 5.808839e+01
SCYL3 4.391144e+01
C1orf112 8.791386e+00
21618 more rows ...
$deviance
[1] 26.195847 7.090188 8.490570 12.459343 9.061801
21618 more elements ...
$iter
[1] 11 18 6 9 18
21618 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
21618 more elements ...
$method
[1] "levenberg"
$counts
X108_Hip_non.sclerotic_adipocyte X108_Hip_sclerotic_adipocyte X125_Hip_non.sclerotic_adipocyte X125_Hip_sclerotic_adipocyte X126_Hip_non.sclerotic_adipocyte X126_Hip_sclerotic_adipocyte
TSPAN6 30 32 35 12 0 20
TNMD 5 8 0 1 2 1
DPM1 67 101 91 51 52 19
SCYL3 30 2 13 20 22 11
C1orf112 6 8 25 16 0 0
X129_Hip_non.sclerotic_adipocyte X129_Hip_sclerotic_adipocyte X143_Hip_non.sclerotic_adipocyte X143_Hip_sclerotic_adipocyte X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte
TSPAN6 0 16 10 8 30 8
TNMD 0 2 0 1 4 0
DPM1 18 42 18 81 112 43
SCYL3 8 8 9 8 86 1
C1orf112 14 6 0 9 4 6
X146_Hip_non.sclerotic_adipocyte X146_Hip_sclerotic_adipocyte X150_Hip_sclerotic_adipocyte X152_Hip_non.sclerotic_adipocyte X152_Hip_sclerotic_adipocyte X153_Hip_non.sclerotic_adipocyte
TSPAN6 38 51 65 1 23 33
TNMD 4 0 0 0 0 2
DPM1 119 174 85 115 119 124
SCYL3 35 50 27 26 89 49
C1orf112 41 40 6 19 55 24
X153_Hip_sclerotic_adipocyte X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X157_Hip_non.sclerotic_adipocyte X157_Hip_sclerotic_adipocyte X158_Hip_non.sclerotic_adipocyte
TSPAN6 38 19 0 67 7 11
TNMD 0 0 0 1 9 0
DPM1 148 40 12 160 56 3
SCYL3 54 20 10 71 31 10
C1orf112 37 9 3 67 3 0
X158_Hip_sclerotic_adipocyte
TSPAN6 74
TNMD 0
DPM1 94
SCYL3 56
C1orf112 15
21618 more rows ...
$unshrunk.coefficients
(Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 groupHSA
TSPAN6 -12.16412 -0.5489509 -0.4635492 -1.2886140 -0.22261836 -0.56764256 -0.3740848 0.4322601 -2.0303984 -0.6433719 -1.0083028 -0.58857573 0.56195233 0.07919987
TNMD -13.77429 -3.0407553 -1.0142583 -1.7565369 -1.95020357 -1.43778230 -1.6667164 -19.4313043 -19.3533944 -2.5913812 -19.3653254 -0.07177878 -19.31629685 0.10990627
DPM1 -11.19489 -0.4485234 -0.4482134 -0.7366739 0.16251188 -0.05673116 -0.1612390 -0.2697678 -0.4574175 -0.2704057 -0.7545501 -0.21653053 -0.48292611 0.08026075
SCYL3 -12.65978 -0.3212348 0.4659547 -0.3062402 0.32583988 0.51463711 0.2761429 0.4410296 0.4034899 0.4438473 0.4722246 0.81149270 1.09489458 -0.31246045
C1orf112 -13.70083 0.7854085 -17.5563597 0.9158003 0.05253689 -0.05924937 1.0788777 -0.4759231 0.7157706 0.7022999 0.2774029 0.77218323 0.07361686 0.14145851
21618 more rows ...
$df.residual
[1] 11 11 11 11 11
21618 more elements ...
$design
(Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 groupHSA
X108_Hip_non.sclerotic_adipocyte 1 0 0 0 0 0 0 0 0 0 0 0 0 0
X108_Hip_sclerotic_adipocyte 1 0 0 0 0 0 0 0 0 0 0 0 0 1
X125_Hip_non.sclerotic_adipocyte 1 1 0 0 0 0 0 0 0 0 0 0 0 0
X125_Hip_sclerotic_adipocyte 1 1 0 0 0 0 0 0 0 0 0 0 0 1
X126_Hip_non.sclerotic_adipocyte 1 0 1 0 0 0 0 0 0 0 0 0 0 0
20 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 15.43908 15.69235 15.77096 16.10605 15.36703 14.82073 14.88684 15.53347 14.20654 15.14467 16.00543 14.89638 16.10394 16.46685 15.82705 16.14883 16.67462 16.35685 16.31579 15.51961 14.51218 16.60281 15.24665 14.22375
[,25]
[1,] 15.65952
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 25
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
21618 more rows ...
$dispersion
[1] 0.5576023 2.8420737 0.2406457 0.5091346 0.9366525
21618 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 1.9934747 -0.8832058 3.4645637 2.1348337 1.1490553
21618 more elements ...
$df.residual.zeros
[1] 11 8 11 11 10
21618 more elements ...
$df.prior
[1] 19.72888 19.72888 19.72888 19.72888 19.72888
21618 more elements ...
$var.post
[1] 1.6937166 1.3084838 0.9635258 1.2365193 1.2100764
21618 more elements ...
$var.prior
[1] 1.310270 1.479689 1.070385 1.294423 1.364113
21618 more elements ...
$samples20 more rows ...
$genes21618 more rows ...
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.9090058
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.994568
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.490907
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 4.021385
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.812784 2.812784
$hip_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 3.689862 3.358340
$hip_adipocytes_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$hip_adipocytes_sclerotic_vs_non_sclerotic$boxplot_gg
$hip_pellet_sclerotic_vs_non_sclerotic
$hip_pellet_sclerotic_vs_non_sclerotic$name
[1] "HSP-vs-HNSP"
$hip_pellet_sclerotic_vs_non_sclerotic$results
Coefficient: groupHSP
$hip_pellet_sclerotic_vs_non_sclerotic$colsums_samples
$hip_pellet_sclerotic_vs_non_sclerotic$normalized_matrix
X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet
TSPAN6 3.705423e+00 3.922387e+00 1.691089e+00 8.441617e-01 0.000000e+00 0.000000e+00
DPM1 1.667441e+01 2.603038e+01 1.050891e+01 1.786809e+01 9.512169e-01 6.216233e+00
SCYL3 9.263559e+00 3.565806e-01 4.831682e+00 5.346357e+00 1.331704e+01 6.216233e+00
C1orf112 6.484491e+00 0.000000e+00 4.831682e+00 4.502196e+00 0.000000e+00 8.288311e+00
FGR 2.223254e+02 2.674354e+02 4.383543e+02 4.727305e+02 1.398289e+02 7.355876e+01
CFH 5.558135e+00 3.565806e-01 3.623761e-01 1.125549e+00 0.000000e+00 3.108117e+00
FUCA2 2.779068e+00 1.426322e+01 1.207920e+01 8.723004e+00 2.853651e+00 1.295049e+01
GCLC 2.223254e+01 2.460406e+01 8.407126e+01 6.767363e+01 1.046339e+01 1.502256e+01
NFYA 3.612788e+01 5.206077e+01 7.549503e+01 4.825791e+01 2.378042e+01 2.641899e+01
STPG1 2.779068e+00 4.278967e+00 5.798018e+00 6.331212e+00 4.756084e+00 5.180194e-01
NIPAL3 9.263559e+00 2.282116e+01 1.763564e+01 1.378797e+01 3.234137e+01 1.761266e+01
LAS1L 5.836042e+01 6.204502e+01 6.607325e+01 4.530334e+01 5.136571e+01 4.506769e+01
ENPP4 7.410847e+00 1.176716e+01 3.140593e+00 4.502196e+00 0.000000e+00 1.036039e+00
SEMA3F 3.705423e+01 4.278967e+01 1.932673e+00 1.421005e+01 3.899989e+01 5.491006e+01
ANKIB1 8.337203e+00 1.604613e+01 1.872277e+01 1.533560e+01 2.473164e+01 3.367126e+01
CYP51A1 8.337203e+00 1.212374e+01 6.039602e+00 5.487051e+00 7.609735e+00 7.252272e+00
KRIT1 3.705423e+00 3.209225e+00 1.727326e+01 1.027063e+01 8.560952e+00 6.734253e+00
RAD52 1.111627e+01 1.069742e+01 1.775643e+01 8.019536e+00 9.512169e-01 1.295049e+01
MYH16 0.000000e+00 0.000000e+00 2.415841e-01 0.000000e+00 0.000000e+00 0.000000e+00
BAD 1.667441e+01 1.426322e+01 1.691089e+01 1.674254e+01 1.141460e+01 2.175682e+01
LAP3 2.315890e+01 3.066593e+01 3.961979e+01 4.192670e+01 1.027314e+02 6.268035e+01
CD99 1.232053e+02 1.757942e+02 6.691879e+01 1.058016e+02 2.577798e+02 2.792125e+02
HS3ST1 8.337203e+00 1.961193e+01 0.000000e+00 5.768438e+00 1.331704e+01 1.916672e+01
AOC1 0.000000e+00 0.000000e+00 2.415841e+00 2.110404e+00 0.000000e+00 0.000000e+00
WNT16 0.000000e+00 3.387516e+01 0.000000e+00 1.899364e+01 0.000000e+00 0.000000e+00
HECW1 0.000000e+00 5.705290e+00 1.087128e+00 0.000000e+00 9.512169e+00 8.288311e+00
MAD1L1 6.484491e+00 1.426322e+01 1.135445e+01 1.238104e+01 2.092677e+01 9.842369e+00
LASP1 1.806394e+02 1.921969e+02 1.485742e+02 1.938758e+02 2.435115e+02 2.072078e+02
SNX11 1.482169e+01 8.914515e+00 1.425346e+01 1.392867e+01 1.807312e+01 7.770291e+00
TMEM176A 1.389534e+01 8.914515e+00 1.062970e+01 9.848553e+00 3.519502e+01 4.195957e+01
M6PR 2.964339e+01 3.173567e+01 6.426137e+01 3.742450e+01 3.043894e+01 3.626136e+01
KLHL13 0.000000e+00 1.426322e+00 2.415841e+00 1.547630e+00 9.512169e-01 1.554058e+00
CYP26B1 6.577127e+01 5.740948e+01 1.328713e+00 1.027063e+01 2.758529e+01 6.837856e+01
ICA1 1.389534e+01 4.278967e+00 1.014653e+01 7.738149e+00 0.000000e+00 1.502256e+01
DBNDD1 0.000000e+00 0.000000e+00 1.691089e+00 2.391791e+00 0.000000e+00 0.000000e+00
ALS2 2.037983e+01 4.992128e+00 1.968910e+01 1.069271e+01 3.804867e+01 2.486493e+01
CASP10 1.018991e+01 1.212374e+01 2.838613e+01 2.532485e+01 2.568286e+01 3.522532e+01
CFLAR 2.955075e+02 3.683478e+02 4.180613e+02 4.134985e+02 4.708523e+02 3.538073e+02
X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet
TSPAN6 0.000000e+00 2.421970e-01 8.271076e-01 6.832711e-01 0.000000e+00 1.095086e+00 2.258421e+00
DPM1 5.095465e+00 1.582354e+01 2.135441e+01 4.099627e+00 1.214842e+00 8.291366e+00 1.219547e+01
SCYL3 0.000000e+00 3.794420e+00 3.383622e+00 1.184337e+01 9.718734e+00 1.251527e+00 2.408982e+00
C1orf112 1.019093e+01 1.453182e+00 3.985155e+00 2.277570e-01 0.000000e+00 5.631871e+00 3.914596e+00
FGR 7.199164e+02 3.657175e+02 3.966357e+02 4.987879e+01 3.097846e+01 1.907014e+02 3.628529e+02
CFH 7.279235e-01 2.421970e-01 3.759580e-01 7.743739e+00 4.251946e+00 1.095086e+00 0.000000e+00
FUCA2 6.551312e+00 1.396669e+01 1.609100e+01 1.480421e+01 2.672652e+01 1.079442e+01 1.851905e+01
GCLC 6.114558e+01 3.786346e+01 6.970261e+01 3.416356e+01 2.065231e+01 6.992907e+01 7.497957e+01
NFYA 4.221956e+01 5.715849e+01 6.143154e+01 2.755860e+01 2.854878e+01 3.770225e+01 6.278410e+01
STPG1 1.383055e+01 2.179773e+00 2.330940e+00 1.594299e+00 3.037104e+00 5.944753e+00 2.107859e+00
NIPAL3 1.455847e+01 3.616808e+01 2.691859e+01 2.140916e+01 2.368941e+01 2.549986e+01 2.559544e+01
LAS1L 6.041765e+01 5.158796e+01 4.857377e+01 3.780767e+01 2.611910e+01 4.364700e+01 3.462912e+01
ENPP4 1.455847e+00 6.781516e+00 5.564178e+00 0.000000e+00 0.000000e+00 1.720850e+00 3.161789e+00
SEMA3F 2.183771e+00 8.073233e+00 4.060346e+00 2.801412e+01 5.223820e+01 1.517476e+01 8.732560e+00
ANKIB1 8.007159e+00 1.550061e+01 1.481275e+01 2.391449e+01 1.761521e+01 1.533121e+01 2.017523e+01
CYP51A1 7.279235e+00 7.669571e+00 1.165470e+01 1.548748e+01 1.154100e+01 6.414076e+00 8.431438e+00
KRIT1 1.965394e+01 9.768612e+00 1.661734e+01 4.327384e+00 3.037104e+00 8.917130e+00 5.871894e+00
RAD52 6.551312e+00 1.219058e+01 1.255700e+01 7.515982e+00 4.859367e+00 1.032510e+01 6.925824e+00
MYH16 0.000000e+00 0.000000e+00 8.271076e-01 0.000000e+00 3.037104e+00 0.000000e+00 7.528069e-01
BAD 1.674224e+01 1.961796e+01 2.045212e+01 3.553010e+01 6.499403e+01 4.223903e+01 3.643586e+01
LAP3 2.183771e+01 3.762127e+01 2.684340e+01 2.118140e+01 3.583783e+01 3.253970e+01 4.652347e+01
CD99 4.149164e+01 1.713140e+02 9.323758e+01 2.480274e+02 3.711342e+02 9.574181e+01 1.187929e+02
HS3ST1 4.367541e+00 7.023713e+00 4.661879e+00 2.095365e+01 1.883005e+01 1.048154e+01 1.806737e+00
AOC1 0.000000e+00 4.843940e-01 1.052682e+00 1.138785e+00 3.644525e+00 1.407968e+00 1.806737e+00
WNT16 0.000000e+00 8.880556e-01 6.015328e-01 5.693926e+00 2.125973e+01 0.000000e+00 4.968526e+00
HECW1 1.091885e+01 4.036617e-01 2.255748e-01 1.366542e+00 2.429684e+00 1.095086e+00 6.022455e-01
MAD1L1 5.823388e+00 1.324010e+01 1.609100e+01 9.338038e+00 7.289051e+00 1.220239e+01 9.635929e+00
LASP1 1.128281e+02 2.354155e+02 1.897084e+02 2.521270e+02 2.277828e+02 2.384159e+02 2.371342e+02
SNX11 1.310262e+01 1.889137e+01 1.970020e+01 1.730953e+01 2.794136e+01 2.018087e+01 2.107859e+01
TMEM176A 0.000000e+00 2.898291e+01 7.443968e+00 7.515982e+01 3.340815e+01 2.190172e+01 2.996172e+01
M6PR 1.528639e+01 4.367619e+01 4.797224e+01 2.801412e+01 2.247457e+01 4.302124e+01 6.805375e+01
KLHL13 8.007159e+00 4.843940e-01 6.015328e-01 1.138785e+00 6.074209e-01 1.720850e+00 2.860666e+00
CYP26B1 0.000000e+00 9.768612e+00 1.954982e+00 5.010655e+01 8.382408e+01 3.598140e+00 9.334806e+00
ICA1 1.164678e+01 9.122753e+00 1.684292e+01 4.327384e+00 6.074209e-01 8.134925e+00 7.979754e+00
DBNDD1 5.823388e+00 2.018308e+00 1.203066e+00 3.188598e+00 7.896471e+00 3.128817e-01 2.107859e+00
ALS2 1.310262e+01 1.784185e+01 1.556466e+01 2.573654e+01 1.822263e+01 1.548765e+01 1.189435e+01
CASP10 1.965394e+01 2.777192e+01 6.090520e+01 2.505327e+01 8.503892e+00 4.161327e+01 3.944708e+01
CFLAR 3.006324e+02 5.315417e+02 4.237047e+02 2.393726e+02 1.779743e+02 2.632900e+02 3.687248e+02
X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet
TSPAN6 0.000000e+00 2.427193e+00 6.589087e-01 7.708632e-01 3.647412e-01 9.909671e-01 0.00000
DPM1 2.138737e+01 9.708770e+00 1.479550e+01 8.993404e+00 1.568387e+01 1.172644e+01 9.31312
SCYL3 0.000000e+00 1.213596e+01 4.193055e+00 5.652997e+00 3.793308e+00 4.129030e+00 0.00000
C1orf112 0.000000e+00 8.090642e-01 3.893551e+00 4.882133e+00 2.115499e+00 1.486451e+00 0.00000
FGR 1.168080e+02 2.831725e+01 2.363685e+02 2.507875e+02 3.456288e+02 3.446914e+02 181.60584
CFH 0.000000e+00 2.427193e+01 5.990079e-02 1.798681e+00 1.531913e+00 2.312257e+00 11.64140
FUCA2 8.225912e+00 2.427193e+01 1.311827e+01 1.207686e+01 1.451670e+01 1.123096e+01 10.47726
GCLC 1.069369e+01 2.669912e+01 1.071026e+02 5.473129e+01 9.140414e+01 6.978060e+01 15.13382
NFYA 3.619401e+01 6.553420e+01 5.037656e+01 4.471006e+01 5.164735e+01 4.219868e+01 32.59592
STPG1 4.112956e+00 6.472513e+00 6.169781e+00 1.541726e+00 4.668687e+00 4.046449e+00 0.00000
NIPAL3 1.645182e+00 2.669912e+01 2.845288e+01 3.571666e+01 3.063826e+01 2.361805e+01 57.04286
LAS1L 4.688770e+01 4.611666e+01 7.098244e+01 4.445311e+01 5.967166e+01 6.928512e+01 68.68426
ENPP4 5.758139e+00 3.236257e+00 2.815337e+00 5.139088e+00 1.677810e+00 1.238709e+00 0.00000
SEMA3F 3.701661e+01 2.912631e+01 3.893551e+00 7.451677e+00 4.522791e+00 4.129030e+00 29.10350
ANKIB1 4.112956e+00 3.155350e+01 1.904845e+01 1.156295e+01 1.685104e+01 2.105805e+01 2.32828
CYP51A1 4.112956e+00 1.132690e+01 6.708888e+00 1.259077e+01 4.376894e+00 9.496768e+00 9.31312
KRIT1 1.809701e+01 4.045321e+00 1.515490e+01 8.736449e+00 9.920961e+00 9.083865e+00 13.96968
RAD52 7.403321e+00 1.294503e+01 1.485540e+01 7.965586e+00 1.911244e+01 1.725934e+01 19.79038
MYH16 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00000
BAD 2.056478e+01 6.067981e+01 1.862915e+01 2.389676e+01 2.027961e+01 2.089289e+01 18.62624
LAP3 2.056478e+01 8.899706e+01 2.839297e+01 2.312590e+01 1.794527e+01 2.873805e+01 25.61108
CD99 2.656970e+02 3.406160e+02 7.421708e+01 6.398164e+01 8.009717e+01 9.430703e+01 225.84316
HS3ST1 4.935547e+00 2.103567e+01 1.916825e+00 2.055635e+00 4.158050e+00 2.725159e+00 34.92420
AOC1 0.000000e+00 0.000000e+00 5.990079e-01 0.000000e+00 1.750758e+00 1.156128e+00 0.00000
WNT16 0.000000e+00 4.530759e+01 0.000000e+00 1.798681e+00 0.000000e+00 1.734192e+00 4.65656
HECW1 1.645182e+00 4.045321e+00 2.396032e-01 7.708632e-01 5.835859e-01 9.083865e-01 0.00000
MAD1L1 9.048504e+00 3.317163e+01 1.922815e+01 1.310467e+01 1.232825e+01 1.494709e+01 9.31312
LASP1 2.204545e+02 2.144020e+02 1.900652e+02 1.793542e+02 1.879147e+02 2.067818e+02 109.42916
SNX11 1.645182e+00 1.051783e+01 1.617321e+01 1.490335e+01 1.612156e+01 1.486451e+01 0.00000
TMEM176A 3.701661e+01 7.686110e+01 5.151468e+00 2.363980e+01 2.261395e+00 5.367738e+00 3.49242
M6PR 4.359734e+01 6.715233e+01 4.977756e+01 3.545971e+01 5.456528e+01 5.086964e+01 47.72974
KLHL13 2.467774e+00 0.000000e+00 7.188095e-01 5.139088e-01 8.024306e-01 6.606447e-01 0.00000
CYP26B1 1.233887e+01 3.478976e+01 1.257917e+00 8.479495e+00 1.458965e-01 7.267092e+00 75.66910
ICA1 8.225912e+00 0.000000e+00 9.284622e+00 8.479495e+00 1.371427e+01 1.593805e+01 13.96968
DBNDD1 8.225912e-01 4.854385e+00 1.737123e+00 2.055635e+00 5.471118e+00 7.101931e+00 0.00000
ALS2 7.403321e+00 4.207134e+01 1.725143e+01 1.695899e+01 2.779328e+01 2.378321e+01 13.96968
CASP10 6.580730e+00 8.899706e+00 2.935139e+01 2.723717e+01 4.530086e+01 5.260384e+01 32.59592
CFLAR 2.986006e+02 8.899706e+01 2.935139e+02 2.410232e+02 4.377624e+02 4.195094e+02 168.80030
X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 0.000000e+00 0.000000e+00 3.208281e+00 8.262523e+00 3.958206e+00 9.413219e+00
DPM1 1.208301e+01 9.309130e+00 1.094590e+01 9.584527e+00 1.741611e+01 2.235639e+01
SCYL3 2.066831e+00 3.324689e+00 5.095506e+00 4.957514e+00 2.691580e+00 1.176652e+00
C1orf112 4.133663e+00 8.865838e-01 5.661673e-01 9.915028e-01 4.749848e-01 2.059142e+00
FGR 4.273572e+02 3.799012e+02 1.560734e+02 1.305479e+02 9.908182e+02 4.471279e+01
CFH 0.000000e+00 1.773168e+00 3.963171e+00 8.923525e+00 6.333130e-01 8.824893e+00
FUCA2 2.098629e+01 1.751003e+01 1.037973e+01 1.454204e+01 1.139963e+01 2.794549e+01
GCLC 6.645658e+01 3.502006e+01 7.926342e+01 2.776208e+01 4.528188e+01 1.764979e+01
NFYA 3.688499e+01 5.053528e+01 4.246255e+01 3.635510e+01 5.842313e+01 2.088558e+01
STPG1 3.338728e+00 2.881397e+00 7.548897e+00 3.635510e+00 5.066504e+00 2.353305e+00
NIPAL3 2.448400e+01 1.795332e+01 2.019330e+01 5.949017e+00 2.137431e+01 3.206378e+01
LAS1L 6.375380e+01 3.745817e+01 3.359259e+01 4.032111e+01 5.446492e+01 3.765288e+01
ENPP4 3.020754e+00 3.324689e+00 1.509779e+00 2.313506e+00 3.958206e+00 8.824893e-01
SEMA3F 2.384806e+00 1.928320e+01 2.434519e+01 3.404159e+01 1.504118e+01 2.647468e+01
ANKIB1 1.748857e+01 9.087484e+00 1.868352e+01 2.280456e+01 9.816352e+00 1.647313e+01
CYP51A1 1.081112e+01 1.352040e+01 1.962713e+01 8.923525e+00 1.060799e+01 6.471588e+00
KRIT1 7.949352e+00 6.871025e+00 1.019101e+01 5.949017e+00 5.699817e+00 6.765751e+00
RAD52 1.033416e+01 7.092671e+00 1.132335e+01 8.593024e+00 1.171629e+01 2.294472e+01
MYH16 1.271896e+00 0.000000e+00 0.000000e+00 3.635510e+00 0.000000e+00 1.176652e+00
BAD 1.383187e+01 2.726245e+01 2.094819e+01 2.710108e+01 2.549085e+01 3.912369e+01
LAP3 2.353008e+01 3.457677e+01 2.755347e+01 4.230412e+01 2.248261e+01 3.471124e+01
CD99 1.195583e+02 1.540439e+02 1.717374e+02 1.735130e+02 9.293869e+01 5.174329e+02
HS3ST1 1.430883e+00 3.324689e+00 1.434290e+01 1.024553e+01 5.858145e+00 2.941631e+00
AOC1 9.221248e+00 3.103043e+00 0.000000e+00 1.983006e+00 0.000000e+00 1.176652e+00
WNT16 0.000000e+00 8.200901e+00 1.773991e+01 5.056664e+01 6.491458e+00 4.706609e+00
HECW1 0.000000e+00 0.000000e+00 0.000000e+00 1.983006e+00 2.216596e+00 4.118283e+00
MAD1L1 1.637566e+01 1.374205e+01 1.245568e+01 1.024553e+01 9.816352e+00 1.264901e+01
LASP1 1.860148e+02 2.243057e+02 1.809848e+02 1.738435e+02 3.005070e+02 2.803374e+02
SNX11 1.573972e+01 1.773168e+01 1.283313e+01 8.593024e+00 1.567450e+01 9.119056e+00
TMEM176A 3.736195e+01 8.489040e+01 9.813566e+00 7.568471e+01 4.116535e+00 1.500232e+01
M6PR 5.612242e+01 7.380810e+01 4.887911e+01 3.701610e+01 4.734015e+01 1.882644e+01
KLHL13 0.000000e+00 2.438106e+00 0.000000e+00 3.305009e-01 7.916413e-01 8.824893e-01
CYP26B1 6.359482e+00 8.422546e+00 2.189180e+01 2.313506e+01 2.374924e+00 4.235948e+01
ICA1 8.585300e+00 2.438106e+00 1.132335e+01 5.949017e+00 1.314125e+01 2.647468e+00
DBNDD1 0.000000e+00 4.432919e-01 5.095506e+00 3.966011e+00 1.424954e+00 1.176652e+00
ALS2 1.717060e+01 1.618016e+01 1.188951e+01 1.421154e+01 1.456620e+01 2.912215e+01
CASP10 2.623286e+01 2.016978e+01 2.547753e+01 1.090653e+01 7.093106e+01 9.119056e+00
CFLAR 6.469183e+02 5.221979e+02 2.700618e+02 2.462232e+02 7.135854e+02 1.185477e+02
[ reached getOption("max.print") -- omitted 22508 rows ]
$hip_pellet_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 patientX79 groupHSP
TSPAN6 -12.740287 -0.98336986 -5.2767541 -3.1422255 -1.5325673 -5.4454023 -0.8824138 -1.31582976 -1.63189193 -1.7990018 -5.44540229 -5.1544555 0.30709634 0.46969393 0.55881924
DPM1 -10.755329 -0.41745530 -1.7118379 -0.6803483 -0.5052503 -2.8647235 -0.7413367 -0.32113750 -0.58240662 -0.4479869 -0.84358389 -0.6945276 -0.73576951 -0.07986831 0.01719896
SCYL3 -12.348296 0.02295286 0.7087225 -0.9030166 0.3438949 0.5208889 -1.0267619 0.08085371 -0.02403484 -0.2251837 -5.56679921 -0.6350010 0.02161326 -0.86444260 0.28822503
C1orf112 -12.688905 0.61990587 0.6962439 0.6616507 -0.2986155 -4.5559621 0.6157417 -1.72809075 0.57845409 -0.3502281 -4.55596210 -0.1022360 -1.14352517 -0.60870929 -0.38200305
FGR -8.000193 0.60595429 -0.9363201 0.6858989 -0.3315575 -1.8660556 0.1734696 -1.39878681 -0.02294180 0.3187415 -0.09810122 0.4604965 -0.58345207 0.46473083 -0.51525569
22541 more rows ...
$fitted.values
X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet
TSPAN6 3.110785 14.49617 8.876079 13.66936 7.563447e-09 2.491245e-08 0.1524839
DPM1 23.001335 60.80191 116.133647 101.45327 4.026045e+00 7.522395e+00 14.8100656
SCYL3 4.659015 16.18633 36.539049 41.95225 9.235434e+00 2.267905e+01 2.3872628
C1orf112 3.300630 5.82979 47.351648 27.63980 6.500934e+00 8.116057e+00 8.1816635
FGR 362.051467 561.79572 5089.661377 2610.00183 1.382174e+02 1.515948e+02 914.8616350
X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6 2.466183 8.119172 4.808088 1.608063e-08 7.535575 14.04482 0.9171965
DPM1 135.874915 170.874785 57.401012 2.000000e+00 64.823067 68.53465 18.7813013
SCYL3 28.785416 80.950823 35.739857 1.600000e+01 9.792487 13.60704 5.6806924
C1orf112 50.155173 30.110502 6.758517 1.882443e-07 36.399830 25.71413 0.6337894
FGR 4926.989553 3201.482006 631.301115 5.100000e+01 2550.025935 1582.59275 100.6350555
X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet
TSPAN6 1.6727331 9.185144 3.840835 6.313026 10.00317 8.390625e-09 4.610174e-08
DPM1 19.4299118 198.530978 47.092183 186.515852 167.64732 8.000000e+00 6.685012e+01
SCYL3 7.7238955 70.277558 21.909233 47.150432 55.70017 1.654383e-07 1.431573e+01
C1orf112 0.4381088 91.607774 14.519267 29.479757 17.70503 9.822203e-08 1.736900e+01
FGR 61.1136700 5472.050088 761.929042 6323.678807 3336.52663 1.560000e+02 3.343405e+03
X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 5.931744e-08 20.705406 21.207903 29.07056 28.066405
DPM1 4.879195e+01 54.036840 31.396759 124.23659 68.039921
SCYL3 1.373250e+01 23.357490 17.836557 11.41194 8.214169
C1orf112 8.470568e+00 5.074451 1.970043 10.45415 3.825557
FGR 1.432448e+03 991.518645 338.173590 3371.40322 1083.849320
22541 more rows ...
$deviance
[1] 2.793172 10.384298 16.817280 16.698857 36.603176
22541 more elements ...
$iter
[1] 19 7 17 17 11
22541 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
22541 more elements ...
$method
[1] "levenberg"
$counts
X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet
TSPAN6 4 11 14 6 0 0 0
DPM1 18 73 87 127 1 12 7
SCYL3 10 1 40 38 14 12 0
C1orf112 7 0 40 32 0 16 14
FGR 240 750 3629 3360 147 142 989
X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6 3 11 3 0 7 15 0
DPM1 196 284 18 2 53 81 26
SCYL3 47 45 52 16 8 16 0
C1orf112 18 53 1 0 36 26 0
FGR 4530 5275 219 51 1219 2410 142
X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet
TSPAN6 3 11 3 5 12 0 0
DPM1 12 247 35 215 142 8 76
SCYL3 15 70 22 52 50 0 13
C1orf112 1 65 19 29 18 0 26
FGR 35 3946 976 4738 4174 156 2688
X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 0 17 25 25 32
DPM1 42 58 29 110 76
SCYL3 15 27 15 17 4
C1orf112 4 3 3 3 7
FGR 1714 827 395 6258 152
22541 more rows ...
$unshrunk.coefficients
(Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 patientX79 groupHSP
TSPAN6 -12.757132 -0.9887031 -19.8083301 -3.2566338 -1.5518658 -20.0868731 -0.8938202 -1.34010758 -1.65585639 -1.8337681 -20.08685760 -19.7897259 0.30453865 0.46826294 0.58431126
DPM1 -10.756455 -0.4179986 -1.7162842 -0.6813077 -0.5058401 -2.8818124 -0.7424711 -0.32148954 -0.58317586 -0.4485443 -0.84500206 -0.6955349 -0.73686737 -0.07995256 0.01737079
SCYL3 -12.353203 0.0223894 0.7107271 -0.9097191 0.3438188 0.5210835 -1.0357690 0.07946997 -0.02492036 -0.2269692 -17.21565672 -0.6398806 0.02113243 -0.87073217 0.29066454
C1orf112 -12.697894 0.6263001 0.7043160 0.6667196 -0.3004584 -16.7158447 0.6218703 -1.76895105 0.58483391 -0.3519180 -16.71583860 -0.1018623 -1.16087620 -0.61370289 -0.38583070
FGR -8.000221 0.6059922 -0.9364748 0.6859240 -0.3316362 -1.8666510 0.1734921 -1.39908477 -0.02294654 0.3187617 -0.09810467 0.4605228 -0.58352979 0.46470992 -0.51534626
22541 more rows ...
$df.residual
[1] 11 11 11 11 11
22541 more elements ...
$design
(Intercept) patientX125 patientX126 patientX129 patientX143 patientX145 patientX146 patientX150 patientX152 patientX153 patientX154 patientX157 patientX158 patientX79 groupHSP
X108_Hip_non.sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X108_Hip_sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1
X125_Hip_non.sclerotic_pellet 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
X125_Hip_sclerotic_pellet 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1
X126_Hip_non.sclerotic_pellet 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
21 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 13.89201 14.84671 15.9292 15.77668 13.86552 14.47325 14.13307 16.33213 16.40323 15.29499 14.31404 15.67059 15.70889 14.01081 14.02739 16.63058 15.17437 16.43352 16.30949 13.66353 15.65444 15.32218 15.48299 14.92266
[,25] [,26]
[1,] 15.6586 15.03913
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 26
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
22541 more rows ...
$dispersion
[1] 1.2941672 0.3067184 0.6271888 0.9164669 0.1527956
22541 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 1.079363 3.670427 2.294829 1.648604 8.148595
22541 more elements ...
$df.residual.zeros
[1] 9 11 11 11 11
22541 more elements ...
$df.prior
[1] 22.577519 22.577519 22.577519 22.577519 1.078782
22541 more elements ...
$var.post
[1] 1.063867 1.055797 1.393853 1.415116 3.083415
22541 more elements ...
$var.prior
[1] 1.3642386 1.1102524 1.3280847 1.3649516 0.5939256
22541 more elements ...
$samples21 more rows ...
$genes22541 more rows ...
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.8259643
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.9538669
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 1.868611
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.207767
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$text
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.168457 2.168457
$hip_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 0.8898118 0.5718562
$hip_pellet_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$hip_pellet_sclerotic_vs_non_sclerotic$boxplot_gg
$hip_sclerotic_vs_non_sclerotic
$hip_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"
$hip_sclerotic_vs_non_sclerotic$results
Coefficient: groupsclerotic
$hip_sclerotic_vs_non_sclerotic$colsums_samples
$hip_sclerotic_vs_non_sclerotic$normalized_matrix
X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet
TSPAN6 6.136374e+00 3.657106e+00 5.182608e+00 3.872889e+00 4.959875e+00 1.670471e+00
TNMD 1.022729e+00 0.000000e+00 1.295652e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.370457e+01 1.645698e+01 1.635761e+01 2.570190e+01 1.289568e+01 1.038078e+01
SCYL3 6.136374e+00 9.142766e+00 3.239130e-01 3.520808e-01 1.842239e+00 4.772773e+00
C1orf112 1.227275e+00 6.399936e+00 1.295652e+00 0.000000e+00 3.542768e+00 4.772773e+00
FGR 9.429562e+01 2.194264e+02 8.502717e+01 2.640606e+02 1.424193e+02 4.330098e+02
CFH 6.136374e+00 5.485660e+00 6.478260e+00 3.520808e-01 1.417107e+00 3.579580e-01
FUCA2 1.615912e+01 2.742830e+00 8.583695e+00 1.408323e+01 1.615502e+01 1.193193e+01
GCLC 4.009098e+01 2.194264e+01 4.372826e+01 2.429357e+01 6.065219e+01 8.304625e+01
NFYA 3.334097e+01 3.565679e+01 4.583369e+01 5.140380e+01 3.812018e+01 7.457458e+01
STPG1 1.206820e+01 2.742830e+00 1.133696e+01 4.224970e+00 3.826189e+00 5.727328e+00
NIPAL3 7.977286e+00 9.142766e+00 2.202608e+01 2.253317e+01 1.842239e+01 1.742062e+01
LAS1L 6.463648e+01 5.759943e+01 5.571304e+01 6.126206e+01 6.306127e+01 6.526767e+01
ENPP4 3.272733e+00 7.314213e+00 2.753261e+00 1.161867e+01 8.502643e-01 3.102302e+00
SEMA3F 5.727283e+01 3.657106e+01 5.004456e+01 4.224970e+01 2.607477e+01 1.909109e+00
ANKIB1 2.863641e+01 8.228489e+00 2.364565e+01 1.584364e+01 2.961754e+01 1.849450e+01
CYP51A1 1.043184e+01 8.228489e+00 1.603369e+01 1.197075e+01 1.162028e+01 5.965966e+00
KRIT1 1.084093e+01 3.657106e+00 9.393477e+00 3.168727e+00 9.069486e+00 1.706266e+01
RAD52 7.568195e+00 1.097132e+01 1.133696e+01 1.056242e+01 1.417107e+01 1.753994e+01
X125_Hip_sclerotic_adipocyte X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet
TSPAN6 1.173139e+00 8.341759e-01 0.000000e+00 0.000000e+00 7.419682e+00 0.000000e+00
TNMD 9.776156e-02 0.000000e+00 4.302316e-01 0.000000e+00 3.709841e-01 0.000000e+00
DPM1 4.985839e+00 1.765672e+01 1.118602e+01 9.390996e-01 7.048698e+00 6.134758e+00
SCYL3 1.955231e+00 5.283114e+00 4.732548e+00 1.314739e+01 4.080825e+00 6.134758e+00
C1orf112 1.564185e+00 4.448938e+00 0.000000e+00 0.000000e+00 0.000000e+00 8.179677e+00
FGR 5.664305e+02 4.671385e+02 9.766257e+01 1.380476e+02 3.709841e+01 7.259463e+01
CFH 2.052993e+00 1.112234e+00 1.936042e+00 0.000000e+00 0.000000e+00 3.067379e+00
FUCA2 1.965007e+01 8.619817e+00 2.258716e+01 2.817299e+00 2.114609e+01 1.278075e+01
GCLC 5.738603e+01 6.687310e+01 2.344762e+01 1.033010e+01 1.372641e+01 1.482566e+01
NFYA 4.985839e+01 4.768705e+01 4.130223e+01 2.347749e+01 4.526006e+01 2.607272e+01
STPG1 4.790316e+00 6.256319e+00 2.366274e+00 4.695498e+00 2.967873e+00 5.112298e-01
NIPAL3 1.300229e+01 1.362487e+01 1.290695e+01 3.192939e+01 1.038755e+01 1.738181e+01
LAS1L 4.575241e+01 4.476744e+01 4.173247e+01 5.071138e+01 5.193777e+01 4.447699e+01
ENPP4 1.564185e+00 4.448938e+00 6.023242e+00 0.000000e+00 2.967873e+00 1.022460e+00
SEMA3F 1.564185e+01 1.404196e+01 1.161625e+01 3.850308e+01 7.048698e+00 5.419036e+01
ANKIB1 2.248516e+01 1.515419e+01 2.387785e+01 2.441659e+01 2.671086e+01 3.322994e+01
CYP51A1 1.094929e+01 5.422143e+00 7.098821e+00 7.512797e+00 1.892019e+01 7.157217e+00
KRIT1 1.583737e+01 1.014914e+01 1.075579e+01 8.451896e+00 1.780724e+01 6.645988e+00
RAD52 5.474647e+00 7.924671e+00 8.174400e+00 9.390996e-01 1.409740e+01 1.278075e+01
X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet
TSPAN6 0.000000e+00 0.000000e+00 2.931600e+00 2.393611e-01 6.483222e+00 8.172430e-01
TNMD 0.000000e+00 0.000000e+00 3.664501e-01 0.000000e+00 0.000000e+00 1.485896e-01
DPM1 5.960540e+00 5.030144e+00 7.695451e+00 1.563826e+01 1.166980e+01 2.109973e+01
SCYL3 2.649129e+00 0.000000e+00 1.465800e+00 3.749991e+00 5.834900e+00 3.343267e+00
C1orf112 4.635975e+00 1.006029e+01 1.099350e+00 1.436167e+00 0.000000e+00 3.937625e+00
FGR 4.377685e+02 7.106874e+02 4.316782e+02 3.614353e+02 2.022765e+02 3.919052e+02
CFH 0.000000e+00 7.185919e-01 0.000000e+00 2.393611e-01 0.000000e+00 3.714741e-01
FUCA2 9.271951e+00 6.467327e+00 1.850573e+01 1.380316e+01 2.398792e+01 1.589909e+01
GCLC 5.364486e+01 6.036172e+01 6.138039e+01 3.742012e+01 4.732752e+01 6.887129e+01
NFYA 2.880928e+01 4.167833e+01 3.921016e+01 5.648922e+01 2.528457e+01 6.069886e+01
STPG1 4.635975e+00 1.365325e+01 0.000000e+00 2.154250e+00 9.076511e+00 2.303139e+00
NIPAL3 1.953733e+01 1.437184e+01 1.392510e+01 3.574459e+01 1.750470e+01 2.659754e+01
LAS1L 6.059882e+01 5.964313e+01 5.753266e+01 5.098392e+01 3.436108e+01 4.799445e+01
ENPP4 0.000000e+00 1.437184e+00 2.198700e+00 6.702111e+00 1.491141e+01 5.497816e+00
SEMA3F 9.934233e+00 2.155776e+00 1.612380e+01 7.978704e+00 1.815302e+01 4.011920e+00
ANKIB1 2.218645e+01 7.904511e+00 2.271990e+01 1.531911e+01 2.009799e+01 1.463608e+01
CYP51A1 6.953963e+00 7.185919e+00 8.061901e+00 7.579768e+00 0.000000e+00 1.151570e+01
KRIT1 1.092766e+01 1.940198e+01 1.502445e+01 9.654231e+00 5.834900e+00 1.641915e+01
RAD52 2.351102e+01 6.467327e+00 2.033798e+01 1.204784e+01 9.724833e+00 1.240723e+01
X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte
TSPAN6 2.181492e+00 6.746903e-01 3.631162e+00 2.791457e+00 0.000000e+00 3.900121e+00
TNMD 2.726866e-01 0.000000e+00 4.841549e-01 0.000000e+00 0.000000e+00 4.105390e-01
DPM1 2.208761e+01 4.048142e+00 1.355634e+01 1.500408e+01 1.199176e+00 1.221354e+01
SCYL3 2.181492e+00 1.169463e+01 1.040933e+01 3.489321e-01 9.593405e+00 3.592217e+00
C1orf112 2.454179e+00 2.248968e-01 4.841549e-01 2.093593e+00 0.000000e+00 4.208025e+00
FGR 6.599015e+01 4.925239e+01 1.101452e+01 2.023806e+01 3.057898e+01 1.529258e+02
CFH 1.636119e+00 7.646490e+00 1.573503e+00 8.723303e+00 4.197115e+00 1.231617e+00
FUCA2 1.554313e+01 1.461829e+01 1.476673e+01 2.128486e+01 2.638186e+01 2.288755e+01
GCLC 2.399642e+01 3.373451e+01 3.812720e+01 1.639981e+01 2.038599e+01 6.404409e+01
NFYA 4.499328e+01 2.721251e+01 3.473812e+01 4.187186e+01 2.818063e+01 5.193319e+01
STPG1 2.454179e+00 1.574277e+00 1.391945e+01 1.256156e+01 2.997939e+00 4.823834e+00
NIPAL3 1.445239e+01 2.114030e+01 2.251320e+01 9.421168e+00 2.338392e+01 2.442707e+01
LAS1L 3.190433e+01 3.733286e+01 5.821963e+01 5.233982e+01 2.578228e+01 4.361977e+01
ENPP4 1.090746e+00 0.000000e+00 4.357394e+00 6.978643e-01 0.000000e+00 4.926468e+00
SEMA3F 1.990612e+01 2.766230e+01 3.122799e+01 2.372739e+01 5.156455e+01 2.093749e+01
ANKIB1 1.745194e+01 2.361416e+01 4.006382e+01 3.454428e+01 1.738805e+01 2.483761e+01
CYP51A1 1.036209e+01 1.529298e+01 6.051937e+00 9.770100e+00 1.139217e+01 6.979164e+00
KRIT1 7.362537e+00 4.273038e+00 1.331426e+01 7.676507e+00 2.997939e+00 1.334252e+01
RAD52 1.608851e+01 7.421593e+00 1.077245e+01 6.629711e+00 4.796702e+00 1.385569e+01
X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet
TSPAN6 1.082135e+00 3.561243e+00 2.227513e+00 0.000000e+00 9.144607e+00 2.396549e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 8.193307e+00 1.215012e+01 1.202857e+01 2.111086e+01 1.195833e+01 9.586196e+00
SCYL3 1.236726e+00 3.491415e+00 2.376014e+00 0.000000e+00 3.798529e+00 1.198275e+01
C1orf112 5.565265e+00 2.793132e+00 3.861023e+00 0.000000e+00 8.441176e-01 7.988497e-01
FGR 1.884461e+02 2.284782e+02 3.578871e+02 1.152978e+02 2.870000e+01 2.795974e+01
CFH 1.082135e+00 1.536223e+00 0.000000e+00 0.000000e+00 2.391666e+00 2.396549e+01
FUCA2 1.066676e+01 1.249927e+01 1.826561e+01 8.119561e+00 1.547549e+01 2.396549e+01
GCLC 6.910204e+01 8.058186e+01 7.395343e+01 1.055543e+01 2.884068e+01 2.636204e+01
NFYA 3.725636e+01 5.753852e+01 6.192486e+01 3.572607e+01 2.870000e+01 6.470682e+01
STPG1 5.874446e+00 3.631072e+00 2.079012e+00 4.059780e+00 2.813725e+00 6.390797e+00
NIPAL3 2.519828e+01 2.045969e+01 2.524515e+01 1.623912e+00 9.848038e+00 2.636204e+01
LAS1L 4.313080e+01 4.322372e+01 3.415520e+01 4.628150e+01 3.728186e+01 4.553443e+01
ENPP4 1.700498e+00 4.259526e+00 3.118518e+00 5.683693e+00 7.034313e+00 3.195399e+00
SEMA3F 1.499530e+01 2.164677e+01 8.613050e+00 3.653802e+01 1.927402e+01 2.875859e+01
ANKIB1 1.514989e+01 2.842012e+01 1.989912e+01 4.059780e+00 2.813725e+01 3.115514e+01
CYP51A1 6.338219e+00 8.239740e+00 8.316049e+00 4.059780e+00 8.722548e+00 1.118390e+01
KRIT1 8.811670e+00 7.820770e+00 5.791534e+00 1.786303e+01 1.631961e+01 3.994248e+00
RAD52 1.020299e+01 9.147508e+00 6.831040e+00 7.307605e+00 1.392794e+01 1.278159e+01
X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte X153_Hip_non.sclerotic_pellet
TSPAN6 9.764704e-02 6.525487e-01 1.352079e+00 7.610445e-01 2.599881e+00 3.608779e-01
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.575685e-01 0.000000e+00
DPM1 1.122941e+01 1.465268e+01 6.995539e+00 8.878853e+00 9.769249e+00 1.551775e+01
SCYL3 2.538823e+00 4.152582e+00 5.231958e+00 5.580993e+00 3.860429e+00 3.753131e+00
C1orf112 1.855294e+00 3.855969e+00 3.233232e+00 4.819949e+00 1.890822e+00 2.093092e+00
FGR 3.861940e+02 2.340870e+02 3.816390e+02 2.475931e+02 1.381876e+02 3.419679e+02
CFH 0.000000e+00 5.932261e-02 5.290744e-01 1.775771e+00 1.418117e+00 1.515687e+00
FUCA2 1.552588e+01 1.299165e+01 1.975211e+01 1.192303e+01 2.024756e+01 1.436294e+01
GCLC 9.256939e+01 1.060688e+02 1.270954e+02 5.403416e+01 6.940894e+01 9.043601e+01
NFYA 6.796234e+01 4.989031e+01 5.913876e+01 4.414058e+01 3.923457e+01 5.110032e+01
STPG1 4.003529e+00 6.110228e+00 4.938027e+00 1.522089e+00 7.563290e+00 4.619238e+00
NIPAL3 3.583646e+01 2.817824e+01 3.409590e+01 3.526173e+01 2.954410e+01 3.031375e+01
LAS1L 5.204587e+01 7.029729e+01 6.554644e+01 4.388690e+01 4.561609e+01 5.903963e+01
ENPP4 4.101176e+00 2.788162e+00 6.172534e+00 5.073630e+00 4.727056e+00 1.660039e+00
SEMA3F 6.932940e+00 3.855969e+00 4.820455e+00 7.356764e+00 2.237473e+01 4.474886e+00
ANKIB1 1.093647e+01 1.886459e+01 2.322049e+01 1.141567e+01 2.426555e+01 1.667256e+01
CYP51A1 3.612940e+00 6.644132e+00 5.878604e+00 1.243039e+01 1.024195e+01 4.330535e+00
KRIT1 1.044823e+01 1.500862e+01 1.210992e+01 8.625171e+00 7.169368e+00 9.815880e+00
RAD52 1.093647e+01 1.471201e+01 8.523976e+00 7.864127e+00 8.114780e+00 1.891000e+01
X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte
TSPAN6 3.166526e+00 9.816047e-01 3.477854e+00 0.000000e+00 0.000000e+00 4.128843e+00
TNMD 0.000000e+00 3.272016e-01 0.000000e+00 0.000000e+00 0.000000e+00 6.162452e-02
DPM1 1.233278e+01 1.161566e+01 7.321799e+00 5.892579e+00 9.193218e+00 9.859923e+00
SCYL3 4.499799e+00 4.090020e+00 3.660899e+00 4.910483e+00 0.000000e+00 4.375341e+00
C1orf112 3.083196e+00 1.472407e+00 1.647405e+00 1.473145e+00 0.000000e+00 4.128843e+00
FGR 1.044953e+02 3.414348e+02 1.365515e+02 1.301278e+02 1.792678e+02 2.085374e+02
CFH 3.749833e+00 2.290411e+00 7.321799e-01 0.000000e+00 1.149152e+01 4.128843e+00
FUCA2 1.416604e+01 1.112485e+01 8.603114e+00 1.031201e+01 1.034237e+01 1.996634e+01
GCLC 5.008110e+01 6.912133e+01 6.260138e+01 6.874676e+01 1.493898e+01 1.181342e+02
NFYA 4.074818e+01 4.180000e+01 3.789031e+01 5.156007e+01 3.217626e+01 4.270579e+01
STPG1 4.749788e+00 4.008219e+00 7.321799e-01 4.910483e-01 0.000000e+00 4.991586e+00
NIPAL3 1.974912e+01 2.339491e+01 2.983633e+01 3.191814e+01 5.630846e+01 2.317082e+01
LAS1L 5.516421e+01 6.863053e+01 5.564567e+01 4.468539e+01 6.779998e+01 5.003911e+01
ENPP4 4.999777e+00 1.227006e+00 2.379585e+00 0.000000e+00 0.000000e+00 3.204475e+00
SEMA3F 2.641549e+01 4.090020e+00 3.624290e+01 1.129411e+01 2.872881e+01 1.867223e+01
ANKIB1 2.274899e+01 2.085910e+01 2.800588e+01 1.571354e+01 2.298304e+00 2.255457e+01
CYP51A1 9.416247e+00 9.407045e+00 2.013495e+00 1.964193e+00 9.193218e+00 5.238084e+00
KRIT1 5.666414e+00 8.998043e+00 9.884428e+00 9.820965e+00 1.378983e+01 1.041454e+01
RAD52 1.083285e+01 1.709628e+01 7.504844e+00 3.928386e+00 1.953559e+01 1.281790e+01
X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte
TSPAN6 0.000000e+00 1.655888e+00 0.000000e+00 7.530164e+00 3.168995e+00 1.200208e+01
TNMD 0.000000e+00 2.128999e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.193856e+01 1.324710e+01 9.195299e+00 2.053681e+00 1.081186e+01 1.524588e+01
SCYL3 2.042121e+00 7.333218e+00 3.284035e+00 6.845604e+00 5.033109e+00 9.082654e+00
C1orf112 4.084243e+00 7.096663e-01 8.757428e-01 0.000000e+00 5.592343e-01 2.432854e+00
FGR 4.222479e+02 1.627501e+02 3.752558e+02 3.696626e+01 1.541623e+02 3.714157e+01
CFH 0.000000e+00 0.000000e+00 1.751486e+00 0.000000e+00 3.914640e+00 2.757234e+00
FUCA2 2.073539e+01 1.324710e+01 1.729592e+01 6.845604e-01 1.025263e+01 1.573245e+01
GCLC 6.566205e+01 5.535397e+01 3.459184e+01 6.571780e+01 7.829281e+01 4.119633e+01
NFYA 3.644401e+01 4.778420e+01 4.991734e+01 5.476483e+00 4.194257e+01 4.184509e+01
STPG1 3.298811e+00 4.021442e+00 2.846164e+00 0.000000e+00 7.456458e+00 1.362398e+01
NIPAL3 2.419128e+01 1.182777e+01 1.773379e+01 1.095297e+01 1.994602e+01 1.070456e+01
LAS1L 6.299159e+01 4.139720e+01 3.700013e+01 5.476483e+01 3.318124e+01 4.800832e+01
ENPP4 2.984639e+00 8.515996e+00 3.284035e+00 0.000000e+00 1.491292e+00 3.243805e-01
SEMA3F 2.356294e+00 2.483832e+01 1.904741e+01 6.297955e+01 2.404708e+01 3.697938e+01
ANKIB1 1.727949e+01 2.602110e+01 8.976364e+00 1.506033e+01 1.845473e+01 4.152071e+01
CYP51A1 1.068187e+01 5.440775e+00 1.335508e+01 1.232209e+01 1.938679e+01 2.351759e+01
KRIT1 7.854313e+00 1.135466e+01 6.787007e+00 8.899285e+00 1.006622e+01 1.265084e+01
RAD52 1.021061e+01 4.257998e+00 7.005942e+00 1.163753e+01 1.118469e+01 8.596084e+00
X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 8.158025e+00 3.911500e+00 9.292487e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.463308e+00 1.721060e+01 2.206966e+01
SCYL3 4.894815e+00 2.659820e+00 1.161561e+00
C1orf112 9.789629e-01 4.693800e-01 2.032731e+00
FGR 1.288968e+02 9.791268e+02 4.413931e+01
CFH 8.810666e+00 6.258401e-01 8.711706e+00
FUCA2 1.435812e+01 1.126512e+01 2.758707e+01
GCLC 2.741096e+01 4.474756e+01 1.742341e+01
NFYA 3.589531e+01 5.773375e+01 2.061771e+01
STPG1 3.589531e+00 5.006720e+00 2.323122e+00
NIPAL3 5.873778e+00 2.112210e+01 3.165253e+01
LAS1L 3.981116e+01 5.382225e+01 3.716995e+01
ENPP4 2.284247e+00 3.911500e+00 8.711706e-01
SEMA3F 3.361106e+01 1.486370e+01 2.613512e+01
ANKIB1 2.251615e+01 9.700521e+00 1.626185e+01
CYP51A1 8.810666e+00 1.048282e+01 6.388585e+00
KRIT1 5.873778e+00 5.632561e+00 6.678975e+00
RAD52 8.484345e+00 1.157804e+01 2.265044e+01
[ reached getOption("max.print") -- omitted 24217 rows ]
$hip_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) batchX125 batchX126 batchX129 batchX143 batchX145 batchX146 batchX150 batchX152 batchX153 batchX154 batchX157 batchX158 batchX79 groupsclerotic
TSPAN6 -12.33137 -0.74791232 -0.96087551 -1.7390972 -0.6658406 -0.7372784 -0.5685940 -0.2252624 -1.8982352 -0.99280749 -1.1574732 -1.1134907 0.4550240 0.28920498 0.167194394
TNMD -14.39331 -2.66463827 -0.93490153 -1.7132316 -1.5560487 -1.0402376 -1.5376495 -3.5476169 -3.4609786 -1.52235863 -3.4588215 -0.2141448 -3.4894572 -3.45333113 0.222145494
DPM1 -10.93500 -0.45117712 -0.99602745 -0.7205204 -0.1943065 -0.5728656 -0.4794864 -0.2438546 -0.5402957 -0.37982433 -0.8957897 -0.4879768 -0.6287768 0.08400982 0.023396235
SCYL3 -12.48798 -0.07986258 0.60149968 -0.5715893 0.4258639 0.5923505 -0.3307001 0.3235805 0.1511724 0.07684324 -0.1945072 0.1237574 0.5433720 -0.65359876 -0.001410283
C1orf112 -13.08304 0.58465196 0.06123562 0.7103485 -0.1249699 -0.7750417 0.7191525 -1.1240017 0.5552093 0.08095515 -0.5150790 0.2001690 -0.5815277 -0.45293591 -0.085067274
24231 more rows ...
$fitted.values
X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte
TSPAN6 21.444640 4.7976851 32.125403 14.777625 14.5958907 17.3349471 25.0959029
TNMD 2.492638 0.5576635 4.503811 2.071745 0.1430746 0.1699239 0.2967056
DPM1 87.040545 19.4730769 112.536102 51.766397 79.9648461 94.9710029 118.6620317
SCYL3 18.339522 4.1029950 23.128962 10.639279 24.4356250 29.0212002 35.3699136
C1orf112 10.059231 2.2504935 11.684098 5.374663 26.1809913 31.0941010 34.9026889
X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet
TSPAN6 17.6467435 7.7403366 1.773048 5.3237113 3.8632572 2.2832984 1.0521882
TNMD 0.2086352 0.8989678 0.205923 0.7457443 0.5411642 0.2291998 0.1056197
DPM1 83.4398524 30.5153217 6.990023 18.1139454 13.1447455 26.1279485 12.0402655
SCYL3 24.8711431 31.9039416 7.308109 18.4729952 13.4052971 6.3753773 2.9378975
C1orf112 24.5426036 10.1721073 2.330084 5.4245805 3.9364549 12.7151000 5.8593648
X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte
TSPAN6 4.8947285 11.240382 3.4627718 30.21734 9.7653693 11.8404772 17.271022
TNMD 0.5926131 1.360892 0.1468117 1.28113 0.4993633 0.6054764 1.480462
DPM1 48.3405609 111.010525 22.6068552 197.27522 55.0231443 66.7153759 82.880739
SCYL3 11.5056229 26.421813 8.8763948 77.45848 21.0736487 25.5517276 56.187173
C1orf112 21.1342228 48.533180 2.8002893 24.43629 6.1230567 7.4241855 7.740460
X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6 7.1062269 4.1354926 24.1238844 16.0161584 42.057926 19.7765419 4.302635e+00
TNMD 0.7346991 0.4275606 0.9968963 0.6618523 2.096243 0.9856987 2.156279e-09
DPM1 29.4316828 17.1278664 107.3229064 71.2530634 161.485484 75.9339496 1.717690e+01
SCYL3 19.4624063 11.3262126 26.2129474 17.4031143 38.472889 18.0907801 6.395888e+00
C1orf112 2.4693826 1.4370655 41.3821792 27.4741631 55.938980 26.3037124 8.076395e-01
X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte
TSPAN6 2.945459e+01 5.187279e+00 6.571185e+00 1.081640e+01 1.294691e+01 3.000210e+00 20.479626
TNMD 1.780387e-08 3.135459e-09 1.953570e-08 3.215643e-08 4.642401e-08 1.075791e-08 1.227007
DPM1 1.014854e+02 1.787271e+01 1.061389e+02 1.747082e+02 1.804835e+02 4.182374e+01 154.490713
SCYL3 3.686020e+01 6.491488e+00 4.473069e+01 7.362824e+01 7.419359e+01 1.719301e+01 51.451613
C1orf112 4.286834e+00 7.549588e-01 3.687878e+01 6.070373e+01 5.633777e+01 1.305525e+01 28.351493
X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte
TSPAN6 22.354821 22.966762 23.396117 7.482972e+00 3.308608e+00 1.413813e+00 23.204272
TNMD 1.339357 1.659648 1.690674 1.026689e-08 5.475217e-09 2.339634e-09 6.215055
DPM1 168.636488 149.527327 152.322686 3.964879e+01 1.513010e+01 6.465294e+00 177.230711
SCYL3 56.162725 48.575252 49.483349 1.686236e+01 6.276652e+00 2.682098e+00 68.952551
C1orf112 30.947467 24.652119 25.112981 6.680843e+00 2.290357e+00 9.787003e-01 40.901361
X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet
TSPAN6 9.102974 7.170116 7.747160 1.010851e+01 3.712158e+01 5.060715e+01 2.515311e+01
TNMD 2.438149 2.316297 2.502711 2.746090e-09 1.008449e-08 1.658176e-08 8.241577e-09
DPM1 69.527136 47.264785 51.068609 1.385587e+01 5.088302e+01 5.986855e+01 2.975627e+01
SCYL3 27.049902 17.936881 19.380423 9.458360e+00 3.473402e+01 3.986381e+01 1.981338e+01
C1orf112 16.045495 9.799335 10.587976 1.668663e+00 6.127847e+00 6.477299e+00 3.219391e+00
X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 3.744719e+01 2.393196e+01
TNMD 1.236318e-08 9.529723e-09
DPM1 1.237747e+02 6.827023e+01
SCYL3 1.241698e+01 6.680569e+00
C1orf112 8.311105e+00 4.118304e+00
24231 more rows ...
$deviance
[1] 54.11683 14.05643 24.70806 34.13150 36.82026
24231 more elements ...
$iter
[1] 11 18 5 6 10
24231 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
24231 more elements ...
$method
[1] "levenberg"
$counts
X108_Hip_non.sclerotic_adipocyte X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_adipocyte X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_adipocyte X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_adipocyte
TSPAN6 30 4 32 11 35 14 12
TNMD 5 0 8 0 0 0 1
DPM1 67 18 101 73 91 87 51
SCYL3 30 10 2 1 13 40 20
C1orf112 6 7 8 0 25 40 16
X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_adipocyte X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_adipocyte X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_adipocyte X129_Hip_non.sclerotic_pellet
TSPAN6 6 0 0 20 0 0 0
TNMD 0 2 0 1 0 0 0
DPM1 127 52 1 19 12 18 7
SCYL3 38 22 14 11 12 8 0
C1orf112 32 0 0 0 16 14 14
X129_Hip_sclerotic_adipocyte X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_adipocyte X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_adipocyte X143_Hip_sclerotic_pellet X145_Hip_non.sclerotic_adipocyte
TSPAN6 16 3 10 11 8 3 30
TNMD 2 0 0 2 1 0 4
DPM1 42 196 18 284 81 18 112
SCYL3 8 47 9 45 8 52 86
C1orf112 6 18 0 53 9 1 4
X145_Hip_sclerotic_adipocyte X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_adipocyte X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_adipocyte X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet
TSPAN6 8 0 38 7 51 15 0
TNMD 0 0 4 0 0 0 0
DPM1 43 2 119 53 174 81 26
SCYL3 1 16 35 8 50 16 0
C1orf112 6 0 41 36 40 26 0
X150_Hip_sclerotic_adipocyte X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_adipocyte X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_adipocyte X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_adipocyte
TSPAN6 65 3 1 11 23 3 33
TNMD 0 0 0 0 0 0 2
DPM1 85 12 115 247 119 35 124
SCYL3 27 15 26 70 89 22 49
C1orf112 6 1 19 65 55 19 24
X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_adipocyte X153_Hip_sclerotic_pellet X154_Hip_non.sclerotic_adipocyte X154_Hip_sclerotic_adipocyte X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_adipocyte
TSPAN6 5 38 12 19 0 0 67
TNMD 0 0 4 0 0 0 1
DPM1 215 148 142 40 12 8 160
SCYL3 52 54 50 20 10 0 71
C1orf112 29 37 18 9 3 0 67
X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_adipocyte X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_adipocyte X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_adipocyte X158_Hip_sclerotic_pellet
TSPAN6 0 7 0 11 17 74 25
TNMD 0 9 0 0 0 0 0
DPM1 76 56 42 3 58 94 29
SCYL3 13 31 15 10 27 56 15
C1orf112 26 3 4 0 3 15 3
X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 25 32
TNMD 0 0
DPM1 110 76
SCYL3 17 4
C1orf112 3 7
24231 more rows ...
$unshrunk.coefficients
(Intercept) batchX125 batchX126 batchX129 batchX143 batchX145 batchX146 batchX150 batchX152 batchX153 batchX154 batchX157 batchX158 batchX79 groupsclerotic
TSPAN6 -12.33700 -0.75173887 -0.96864502 -1.7581010 -0.6698095 -0.7411260 -0.5718876 -0.2275929 -1.9222132 -1.00012282 -1.1639048 -1.1208705 0.4558880 0.28946537 0.170708215
TNMD -14.48913 -3.22473507 -0.96946511 -1.9047503 -1.6783501 -1.0456686 -1.6060655 -19.4895694 -19.4037965 -1.66284233 -19.4187433 -0.2860992 -19.4184444 -19.38987639 0.358118203
DPM1 -10.93610 -0.45179108 -0.99776059 -0.7216158 -0.1945250 -0.5736527 -0.4801472 -0.2441544 -0.5410582 -0.38031868 -0.8973737 -0.4886538 -0.6296805 0.08409741 0.023435910
SCYL3 -12.49342 -0.08002045 0.60405571 -0.5748625 0.4279329 0.5949487 -0.3324202 0.3252512 0.1521688 0.07750480 -0.1950344 0.1246281 0.5458254 -0.65798477 -0.001436905
C1orf112 -13.09398 0.58953874 0.06154321 0.7160522 -0.1251721 -0.7867109 0.7247443 -1.1434759 0.5597130 0.08211036 -0.5203066 0.2029405 -0.5884830 -0.45888961 -0.083726112
24231 more rows ...
$df.residual
[1] 36 36 36 36 36
24231 more elements ...
$design
(Intercept) batchX125 batchX126 batchX129 batchX143 batchX145 batchX146 batchX150 batchX152 batchX153 batchX154 batchX157 batchX158 batchX79 groupsclerotic
X108_Hip_non.sclerotic_adipocyte 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X108_Hip_non.sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X108_Hip_sclerotic_adipocyte 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1
X108_Hip_sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1
X125_Hip_non.sclerotic_adipocyte 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
46 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 15.40247 13.90513 15.63594 14.85941 15.76948 15.94146 16.14073 15.78858 15.35209 13.87834 14.80711 14.48645 14.92072 14.14597 15.51255 16.3439 14.24888 16.41522 15.11494 15.30762 15.92716 14.86839 14.32702 16.09209
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 15.68248 16.47723 15.72268 14.02382 15.77673 14.04009 16.14191 16.64028 16.64936 15.18719 16.35655 16.44416 16.30046 16.31898 15.51353 14.52672 13.67649 16.60221 15.66647 15.25708 15.33449 14.19449 15.49531 15.6345
[,49] [,50] [,51]
[1,] 14.93538 15.67047 15.05204
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 51
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
24231 more rows ...
$dispersion
[1] 1.0143221 5.8528321 0.3673950 0.7130623 1.1664206
24231 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 1.623798 -1.089619 3.571136 2.221472 1.400589
24231 more elements ...
$df.residual.zeros
[1] 36 25 36 36 36
24231 more elements ...
$df.prior
[1] 17.58321 17.58321 17.58321 17.58321 17.58321
24231 more elements ...
$var.post
[1] 1.3991035 0.6415641 0.7757505 1.0198302 1.0738508
24231 more elements ...
$var.prior
[1] 1.1858827 0.7543233 0.9588205 1.1666969 1.1784033
24231 more elements ...
$samples46 more rows ...
$genes24231 more rows ...
$hip_sclerotic_vs_non_sclerotic$mds_plot
$hip_sclerotic_vs_non_sclerotic$mds_plot$rect
$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.459672
$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.9221995
$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 1.509402
$hip_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.714582
$hip_sclerotic_vs_non_sclerotic$mds_plot$text
$hip_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 1.812565 1.812565
$hip_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 1.407183 1.099783
$hip_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$hip_sclerotic_vs_non_sclerotic$boxplot_gg
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$results
Coefficient: groupsclerotic
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$colsums_samples
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$normalized_matrix
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet
TSPAN6 2.656555e-01 9.205954e+00 5.481659e+00 6.903021e+00 7.019917e+00 3.517982e+00
DPM1 1.567368e+01 1.380893e+01 1.837968e+01 6.903021e+00 1.432063e+01 1.348560e+01
SCYL3 5.401662e+00 3.287841e+00 2.257154e+00 6.275473e+00 2.246373e+00 3.517982e+00
C1orf112 6.287181e+00 0.000000e+00 2.902055e+00 0.000000e+00 5.615933e-01 0.000000e+00
FGR 1.183230e+03 2.048325e+02 1.222088e+02 7.028530e+01 1.555614e+02 8.384523e+01
CFH 7.969666e-01 3.616625e+00 1.612253e+00 2.510189e+00 6.551922e-01 4.104312e+00
FUCA2 1.222015e+01 1.906948e+01 6.126560e+00 1.736214e+01 1.057667e+01 2.052156e+01
GCLC 5.118296e+01 1.972704e+01 1.708988e+01 1.045912e+01 2.695648e+01 5.276973e+00
NFYA 6.030380e+01 3.517989e+01 3.998387e+01 3.179573e+01 3.266601e+01 3.928413e+01
STPG1 2.302348e+00 6.246897e+00 3.546956e+00 8.367298e-01 4.867142e+00 1.583092e+01
NIPAL3 1.859589e+01 1.052109e+01 5.159209e+00 1.234176e+01 1.656700e+01 2.873018e+01
LAS1L 5.268834e+01 3.781017e+01 7.448607e+01 2.238252e+01 4.839062e+01 2.345321e+01
ENPP4 1.372554e+01 4.602977e+00 3.224505e+00 3.346919e+00 7.955905e+00 3.517982e+00
SEMA3F 1.505381e+00 2.268610e+01 7.771058e+01 5.229561e+01 5.728252e+01 3.224817e+01
ANKIB1 8.058217e+00 1.380893e+01 1.289802e+01 1.066830e+01 1.656700e+01 9.967615e+00
CYP51A1 6.818492e+00 8.219602e+00 1.322047e+01 8.785663e+00 6.926318e+00 1.055395e+01
KRIT1 1.142319e+01 9.534738e+00 1.708988e+01 1.652541e+01 1.647340e+01 9.381285e+00
X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet
TSPAN6 5.071507e-01 13.99923 2.672109e+00 6.451039e+00 8.433707e-01 8.063157e+00
DPM1 2.015924e+01 29.55393 2.240461e+01 1.319531e+01 1.766118e+01 1.075088e+01
SCYL3 2.028603e+00 10.88829 3.905390e+00 5.571352e+00 1.835572e+00 2.150175e+00
C1orf112 2.916117e+00 0.00000 3.802617e+00 1.172916e+00 3.720753e+00 0.000000e+00
FGR 4.218226e+02 88.66179 3.603236e+02 4.896925e+01 6.631871e+02 1.311607e+02
CFH 7.607260e-01 6.22188 4.110937e-01 4.691665e+00 2.976603e-01 7.525613e+00
FUCA2 1.242519e+01 3.11094 1.891031e+01 4.984894e+00 9.922009e+00 6.450526e+00
GCLC 6.402778e+01 29.55393 4.994788e+01 7.330726e+00 1.044291e+02 1.505123e+01
NFYA 3.867024e+01 27.99846 3.915667e+01 2.697707e+01 5.328119e+01 5.912982e+00
STPG1 3.930418e+00 13.99923 4.624804e+00 1.759374e+00 4.861784e+00 2.150175e+00
NIPAL3 1.825743e+01 18.66564 1.870476e+01 2.140572e+01 1.954636e+01 8.600701e+00
LAS1L 4.057206e+01 40.44222 4.881737e+01 4.105207e+01 6.022659e+01 3.171508e+01
ENPP4 6.085808e+00 4.66641 8.119100e+00 3.518749e+00 3.125433e+00 2.150175e+00
SEMA3F 3.030225e+01 20.22111 9.660701e+00 3.577394e+01 1.031889e+01 3.171508e+01
ANKIB1 1.052338e+01 12.44376 7.399686e+00 2.404478e+01 8.532927e+00 6.450526e+00
CYP51A1 7.860836e+00 0.00000 5.241444e+00 9.676559e+00 8.136047e+00 8.063157e+00
KRIT1 1.026980e+01 3.11094 1.387441e+01 1.143593e+01 1.830611e+01 1.451368e+01
X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet
TSPAN6 9.589878 1.223865e+01 4.798319e+01 8.027498e+00 3.773157e+00 2.969127e+01
DPM1 0.000000 1.398703e+01 4.798319e+00 1.245646e+01 1.207410e+01 1.370366e+01
SCYL3 1.369983 6.702120e+00 6.397759e+00 0.000000e+00 7.546314e-01 4.567888e+00
C1orf112 0.000000 1.165586e+00 0.000000e+00 8.304308e-01 0.000000e+00 1.141972e+00
FGR 87.678883 5.303417e+01 3.198880e+01 1.309313e+02 8.678262e+01 5.595663e+01
CFH 27.399651 2.913965e+00 1.599440e+01 1.107241e+00 1.056484e+01 7.993804e+00
FUCA2 10.959860 1.544402e+01 0.000000e+00 6.920257e+00 5.282420e+00 2.854930e+01
GCLC 31.509599 1.398703e+01 1.279552e+01 1.494775e+01 1.433800e+01 2.055549e+01
NFYA 31.509599 4.283529e+01 3.358824e+01 1.688543e+01 1.131947e+01 4.339493e+01
STPG1 5.479930 1.107307e+01 6.397759e+00 8.304308e+00 2.263894e+00 0.000000e+00
NIPAL3 30.139616 8.159103e+00 2.559104e+01 2.186801e+01 3.018526e+01 1.941352e+01
LAS1L 42.469459 2.826546e+01 4.158544e+01 4.235197e+01 2.490284e+01 2.169747e+01
ENPP4 0.000000 8.159103e+00 4.798319e+00 5.536205e-01 1.509263e+00 0.000000e+00
SEMA3F 28.769634 4.516646e+01 1.759384e+01 4.179835e+01 3.546768e+01 5.595663e+01
ANKIB1 19.179756 9.907482e+00 1.439496e+01 1.522456e+01 9.810209e+00 4.567888e+00
CYP51A1 39.729494 6.410724e+00 0.000000e+00 1.134922e+01 1.131947e+01 6.851832e+00
KRIT1 15.069808 8.741896e+00 0.000000e+00 1.079560e+01 7.546314e-01 1.141972e+01
X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet
TSPAN6 1.447908e+01 5.168783e+00 6.664913e+00 4.256301e+00 3.230201e+00 1.941976e+01
DPM1 1.990873e+01 1.174723e+01 9.873945e+00 1.895989e+01 9.788489e+00 8.091569e+00
SCYL3 9.049423e-01 2.036187e+00 3.702729e+00 5.417111e+00 3.915395e+00 9.709882e+00
C1orf112 9.049423e-01 4.698894e-01 2.468486e-01 4.256301e+00 5.873093e-01 0.000000e+00
FGR 7.601516e+01 5.818797e+01 3.529935e+01 3.405041e+01 4.404820e+01 8.334316e+01
CFH 9.049423e-01 3.054281e+00 2.962184e+00 6.964857e+00 5.187899e+00 8.091569e-01
FUCA2 9.049423e+00 1.613287e+01 2.937499e+01 1.470359e+01 9.886374e+00 2.912965e+01
GCLC 1.719390e+01 2.388604e+01 1.925419e+01 2.553781e+01 2.711411e+01 2.912965e+01
NFYA 1.809885e+01 2.764516e+01 3.233717e+01 3.211573e+01 2.564584e+01 2.184723e+01
STPG1 6.334596e+00 3.994060e+00 9.873945e-01 5.804047e+00 2.447122e+00 1.861061e+01
NIPAL3 4.524712e+00 1.237375e+01 8.639702e+00 4.643238e+00 1.076734e+01 1.537398e+01
LAS1L 5.248666e+01 3.367541e+01 2.517856e+01 2.515087e+01 3.494490e+01 3.803037e+01
ENPP4 9.049423e-01 4.777209e+00 4.196427e+00 1.238197e+01 1.859813e+00 0.000000e+00
SEMA3F 1.990873e+01 4.174184e+01 5.060397e+01 4.565850e+01 7.243482e+01 4.207616e+01
ANKIB1 9.049423e+00 1.683770e+01 1.086134e+01 1.509052e+01 1.174619e+01 1.780145e+01
CYP51A1 1.719390e+01 1.550635e+01 1.950104e+01 1.934682e+01 1.311657e+01 1.861061e+01
KRIT1 3.619769e+00 1.010262e+01 1.061449e+01 1.238197e+01 8.613870e+00 4.854941e+00
X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6 1.558993e+01 1.461662e+00 1.322539e+01 5.796559e+00 9.592093e+00 7.089689e+00
DPM1 9.977557e+00 1.218051e+01 1.098725e+01 9.274495e+00 2.599148e+01 3.038438e+01
SCYL3 2.494389e+00 1.948882e+00 3.255481e+00 4.869110e+00 1.856534e+00 1.012813e+00
C1orf112 1.247195e+00 0.000000e+00 1.220805e+00 0.000000e+00 0.000000e+00 0.000000e+00
FGR 5.820242e+01 6.577478e+01 4.272819e+01 4.335826e+01 1.191276e+02 9.317878e+01
CFH 2.078658e-01 9.257191e+00 4.883221e+00 3.014211e+00 1.237689e+01 1.012813e+01
FUCA2 2.328097e+01 4.872206e+00 1.261499e+01 2.434555e+01 1.856534e+01 0.000000e+00
GCLC 1.746073e+01 7.795529e+00 1.668434e+01 1.808526e+01 1.299574e+01 1.417938e+01
NFYA 2.452816e+01 1.510384e+01 2.767159e+01 1.112939e+01 1.639939e+01 3.443563e+01
STPG1 7.483168e+00 2.923323e+00 5.086689e+00 8.115183e+00 0.000000e+00 9.115315e+00
NIPAL3 1.891579e+01 3.020767e+01 1.403926e+01 1.507105e+01 1.454285e+01 1.519219e+01
LAS1L 2.723042e+01 2.728435e+01 4.008311e+01 3.338818e+01 3.620242e+01 2.025626e+01
ENPP4 4.988779e+00 5.359426e+00 1.831208e+00 2.086761e+00 3.403646e+00 2.025626e+00
SEMA3F 3.970236e+01 2.923323e+01 4.049004e+01 3.918474e+01 3.867780e+01 2.329469e+01
ANKIB1 1.455060e+01 1.023163e+01 1.281846e+01 8.347045e+00 8.044982e+00 6.076877e+00
CYP51A1 1.600566e+01 1.315496e+01 1.098725e+01 2.388182e+01 2.104072e+01 1.823063e+01
KRIT1 1.288768e+01 5.846647e+00 8.952573e+00 1.205684e+01 1.547112e+00 2.126907e+01
X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet X126_Hip_sclerotic_pellet
TSPAN6 3.464896e+00 3.732628e+00 1.733443e+00 8.625461e-01 0.000000 0.000000e+00
DPM1 1.559203e+01 2.477108e+01 1.077211e+01 1.825723e+01 0.889069 5.913613e+00
SCYL3 8.662239e+00 3.393298e-01 4.952693e+00 5.462792e+00 12.446965 5.913613e+00
C1orf112 6.063567e+00 0.000000e+00 4.952693e+00 4.600246e+00 0.000000 7.884818e+00
FGR 2.078937e+02 2.544974e+02 4.493331e+02 4.830258e+02 130.693137 6.997776e+01
CFH 5.197343e+00 3.393298e-01 3.714520e-01 1.150061e+00 0.000000 2.956807e+00
FUCA2 2.598672e+00 1.357319e+01 1.238173e+01 8.912976e+00 2.667207 1.232003e+01
GCLC 2.078937e+01 2.341376e+01 8.617687e+01 6.914745e+01 9.779759 1.429123e+01
NFYA 3.378273e+01 4.954216e+01 7.738583e+01 4.930889e+01 22.226724 2.513286e+01
STPG1 2.598672e+00 4.071958e+00 5.943232e+00 6.469096e+00 4.445345 4.928011e-01
NIPAL3 8.662239e+00 2.171711e+01 1.807733e+01 1.408825e+01 30.228345 1.675524e+01
LAS1L 5.457211e+01 5.904339e+01 6.772808e+01 4.628997e+01 48.009724 4.287370e+01
ENPP4 6.929791e+00 1.119789e+01 3.219251e+00 4.600246e+00 0.000000 9.856022e-01
SEMA3F 3.464896e+01 4.071958e+01 1.981077e+00 1.451953e+01 36.451827 5.223692e+01
ANKIB1 7.796015e+00 1.526984e+01 1.919169e+01 1.566959e+01 23.115793 3.203207e+01
CYP51A1 7.796015e+00 1.153721e+01 6.190867e+00 5.606550e+00 7.112552 6.899215e+00
KRIT1 3.464896e+00 3.053969e+00 1.770588e+01 1.049431e+01 8.001621 6.406414e+00
X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet X146_Hip_sclerotic_pellet
TSPAN6 0.000000e+00 2.364098e-01 8.568633e-01 6.429349e-01 0.000000 1.092095e+00 2.266115e+00
DPM1 5.055205e+00 1.544544e+01 2.212265e+01 3.857610e+00 1.153388 8.268723e+00 1.223702e+01
SCYL3 0.000000e+00 3.703754e+00 3.505350e+00 1.114421e+01 9.227104 1.248109e+00 2.417189e+00
C1orf112 1.011041e+01 1.418459e+00 4.128523e+00 2.143116e-01 0.000000 5.616491e+00 3.927933e+00
FGR 7.142283e+02 3.569788e+02 4.109049e+02 4.693425e+01 29.411396 1.901806e+02 3.640891e+02
CFH 7.221722e-01 2.364098e-01 3.894833e-01 7.286596e+00 4.036858 1.092095e+00 0.000000e+00
FUCA2 6.499549e+00 1.363297e+01 1.666989e+01 1.393026e+01 25.374537 1.076494e+01 1.858214e+01
GCLC 6.066246e+01 3.695874e+01 7.221021e+01 3.214675e+01 19.607597 6.973809e+01 7.523502e+01
NFYA 4.188598e+01 5.579272e+01 6.364157e+01 2.593171e+01 27.104619 3.759929e+01 6.299800e+01
STPG1 1.372127e+01 2.127688e+00 2.414797e+00 1.500181e+00 2.883470 5.928518e+00 2.115041e+00
NIPAL3 1.444344e+01 3.530387e+01 2.788701e+01 2.014529e+01 22.491067 2.543022e+01 2.568264e+01
LAS1L 5.994029e+01 5.035529e+01 5.032125e+01 3.557573e+01 24.797843 4.352780e+01 3.474710e+01
ENPP4 1.444344e+00 6.619475e+00 5.764353e+00 0.000000e+00 0.000000 1.716150e+00 3.172561e+00
SEMA3F 2.166516e+00 7.880328e+00 4.206420e+00 2.636033e+01 49.595687 1.513332e+01 8.762311e+00
ANKIB1 7.943894e+00 1.513023e+01 1.534564e+01 2.250272e+01 16.724127 1.528934e+01 2.024396e+01
CYP51A1 7.221722e+00 7.486311e+00 1.207398e+01 1.457319e+01 10.957187 6.396559e+00 8.460163e+00
KRIT1 1.949865e+01 9.535196e+00 1.721516e+01 4.071921e+00 2.883470 8.892777e+00 5.891899e+00
X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet X154_Hip_sclerotic_pellet
TSPAN6 0.000000e+00 2.318259e+00 6.800126e-01 7.810061e-01 3.793702e-01 1.011839e+00 0.000000e+00
DPM1 1.997198e+01 9.273036e+00 1.526937e+01 9.111738e+00 1.631292e+01 1.197343e+01 8.721136e+00
SCYL3 0.000000e+00 1.159129e+01 4.327353e+00 5.727378e+00 3.945450e+00 4.215997e+00 0.000000e+00
C1orf112 0.000000e+00 7.727530e-01 4.018256e+00 4.946372e+00 2.200347e+00 1.517759e+00 0.000000e+00
FGR 1.090777e+02 2.704635e+01 2.439391e+02 2.540873e+02 3.594912e+02 3.519514e+02 1.700621e+02
CFH 0.000000e+00 2.318259e+01 6.181933e-02 1.822348e+00 1.593355e+00 2.360958e+00 1.090142e+01
FUCA2 7.681531e+00 2.318259e+01 1.353843e+01 1.223576e+01 1.509893e+01 1.146751e+01 9.811278e+00
GCLC 9.985990e+00 2.550085e+01 1.105330e+02 5.545143e+01 9.507018e+01 7.125035e+01 1.417185e+01
NFYA 3.379874e+01 6.259299e+01 5.199006e+01 4.529835e+01 5.371882e+01 4.308749e+01 3.052398e+01
STPG1 3.840765e+00 6.182024e+00 6.367391e+00 1.562012e+00 4.855939e+00 4.131677e+00 0.000000e+00
NIPAL3 1.536306e+00 2.550085e+01 2.936418e+01 3.618662e+01 3.186710e+01 2.411550e+01 5.341696e+01
LAS1L 4.378473e+01 4.404692e+01 7.325591e+01 4.503802e+01 6.206497e+01 7.074443e+01 6.431838e+01
ENPP4 5.377072e+00 3.091012e+00 2.905509e+00 5.206707e+00 1.745103e+00 1.264799e+00 0.000000e+00
SEMA3F 3.456689e+01 2.781911e+01 4.018256e+00 7.549726e+00 4.704191e+00 4.215997e+00 2.725355e+01
ANKIB1 3.840765e+00 3.013737e+01 1.965855e+01 1.171509e+01 1.752690e+01 2.150159e+01 2.180284e+00
CYP51A1 3.840765e+00 1.081854e+01 6.923765e+00 1.275643e+01 4.552443e+00 9.696794e+00 8.721136e+00
KRIT1 1.689937e+01 3.863765e+00 1.564029e+01 8.851402e+00 1.031887e+01 9.275194e+00 1.308170e+01
X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 0.000000e+00 0.000000e+00 3.186183e+00 7.952143e+00 3.971011e+00 9.013019e+00
DPM1 1.187537e+01 9.108305e+00 1.087051e+01 9.224486e+00 1.747245e+01 2.140592e+01
SCYL3 2.031314e+00 3.252966e+00 5.060408e+00 4.771286e+00 2.700288e+00 1.126627e+00
C1orf112 4.062628e+00 8.674576e-01 5.622676e-01 9.542572e-01 4.765213e-01 1.971598e+00
FGR 4.200132e+02 3.717056e+02 1.549984e+02 1.256439e+02 9.940235e+02 4.281184e+01
CFH 0.000000e+00 1.734915e+00 3.935873e+00 8.588315e+00 6.353618e-01 8.449706e+00
FUCA2 2.062565e+01 1.713229e+01 1.030824e+01 1.399577e+01 1.143651e+01 2.675740e+01
GCLC 6.531456e+01 3.426458e+01 7.871746e+01 2.671920e+01 4.542837e+01 1.689941e+01
NFYA 3.625114e+01 4.944509e+01 4.217007e+01 3.498943e+01 5.861212e+01 1.999764e+01
STPG1 3.281354e+00 2.819237e+00 7.496901e+00 3.498943e+00 5.082894e+00 2.253255e+00
NIPAL3 2.406326e+01 1.756602e+01 2.005421e+01 5.725543e+00 2.144346e+01 3.070060e+01
LAS1L 6.265823e+01 3.665008e+01 3.336121e+01 3.880646e+01 5.464111e+01 3.605208e+01
ENPP4 2.968844e+00 3.252966e+00 1.499380e+00 2.226600e+00 3.971011e+00 8.449706e-01
SEMA3F 2.343824e+00 1.886720e+01 2.417750e+01 3.276283e+01 1.508984e+01 2.534912e+01
ANKIB1 1.718804e+01 8.891441e+00 1.855483e+01 2.194792e+01 9.848107e+00 1.577278e+01
CYP51A1 1.062534e+01 1.322873e+01 1.949194e+01 8.588315e+00 1.064231e+01 6.196451e+00
KRIT1 7.812746e+00 6.722797e+00 1.012082e+01 5.725543e+00 5.718256e+00 6.478108e+00
[ reached getOption("max.print") -- omitted 23225 rows ]
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) patientX104 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149 patientX150 patientX151
TSPAN6 -12.642272 0.5325985 -0.080613894 0.3955203 -1.010286258 -5.1385721 0.41050782 -3.0212127 0.3072877 -1.5486785 0.099471185 -5.2559682 -0.8666274 -1.31514557 0.8290270 -1.27287292 1.9373396
DPM1 -11.065634 0.1626920 0.340278139 -0.6954884 0.002112572 -1.3507482 -0.05833726 -0.2856111 0.5133298 -0.1520034 0.180426458 -2.4673866 -0.3478365 0.12286875 -0.9047451 -0.02337654 -0.3983677
SCYL3 -12.384791 -0.6058934 -0.008575266 0.2612114 0.148928373 0.7284506 -0.46629456 -0.7756743 0.2193185 0.4476305 0.043073847 0.6454715 -0.9044528 -0.81019575 -0.8630459 0.19450174 0.3930328
C1orf112 -12.576950 -0.1647928 -0.118073809 -4.0442767 0.864822252 1.0335640 -2.01090884 0.6713779 -0.4881926 -0.3208318 -0.005272773 -4.0442767 0.8033260 0.08188315 -4.7628170 -1.53519923 -1.2890593
FGR -7.167284 -1.8422965 -0.859499288 -1.8374300 -0.176669788 -1.8079688 -1.63001536 -0.1426857 -0.9710598 -1.1383440 -1.237558652 -2.7081297 -0.6248754 -0.15113247 -1.6940841 -2.28031304 -2.6534987
patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX79 patientX99 groupsclerotic
TSPAN6 -1.6188126 -1.74496016 -5.2559682 0.5207178 1.8055717 -5.05918744 0.29963178 0.4198674 -0.01460916 1.5325354 -0.7771552 0.9810127 0.4603485 0.8248522 0.3667191
DPM1 -0.1954187 -0.04664149 -0.4624305 -0.1836762 0.1477250 -0.34266764 -0.38321850 -0.3102676 -0.04850762 -0.4652037 -0.2480437 -0.3754778 0.2838924 0.6497761 -0.1189107
SCYL3 0.1055391 -0.09251174 -5.2953181 -2.8061170 -0.4869201 -0.53994659 0.09863435 -0.4689260 0.04409532 0.3059762 -0.7510566 -0.1091942 -0.7979389 -1.0422844 0.1485874
C1orf112 0.8492516 -0.13561507 -4.0442767 -1.6920664 -0.7388067 -0.07624703 -0.92270464 -1.8196648 -0.18345592 -0.7184476 -4.9545718 -1.5351756 -0.3041042 -4.7929662 -0.9102951
FGR -0.8088230 -0.45966983 -0.9540318 -1.6990193 -2.1062524 -0.36677364 -1.41670610 -2.5550757 -2.62653394 -2.1190526 -2.4616200 -2.5691132 -0.3652631 -1.7045656 -0.5578874
23237 more rows ...
$fitted.values
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6 36.02512 14.099079 17 3.30000e+01 51.753060 12.0050187 34.25763
DPM1 176.35681 42.162972 57 3.30000e+01 157.376731 22.3008306 205.93898
SCYL3 46.93124 14.700769 7 3.00000e+01 27.744714 5.1510976 40.79670
C1orf112 38.62770 4.054426 9 5.00819e-08 4.647315 0.2891173 16.54826
FGR 8711.29982 1342.868580 379 3.36000e+02 1614.501215 147.5130535 2303.82450
X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6 4.0576176 34.39318 17.516388 17 1.369676e+01 7.809351e+00 76.535012
DPM1 14.9006807 182.04472 56.637497 356 1.173077e+01 4.085803e+00 35.957357
SCYL3 3.8675111 42.20258 17.202992 37 3.237621e+00 1.477461e+00 21.161335
C1orf112 0.5256678 33.43625 4.567042 75 2.775474e-08 4.244041e-09 3.179583
FGR 107.4802068 2177.14435 436.741783 13368 2.636735e+02 5.921462e+01 186.280247
X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6 20.2616623 19.5462473 10.4185945 17.168527 31.4822684 62.344617 28.7416089
DPM1 5.8150893 46.9346042 15.2824369 15.856293 17.7618563 146.128865 41.1530316
SCYL3 4.4838462 0.8185068 0.3491892 2.228389 3.2705196 33.068597 12.2017072
C1orf112 0.2257513 2.1970448 0.3140725 1.430976 0.7037373 6.737386 0.8330072
FGR 19.4243722 509.5118019 106.9708043 82.182090 59.3574763 764.842192 138.8830413
X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6 8.156527 46.85196 18.421162 104.199392 3.00000e+00 42.20003 53.811626
DPM1 38.444059 134.89797 12.109176 41.842389 2.50000e+01 52.68636 41.040747
SCYL3 11.224337 51.60311 6.985233 31.624365 4.00000e+00 18.28978 18.666567
C1orf112 7.378633 11.36694 2.084298 3.161937 2.15032e-08 3.49239 1.194349
FGR 144.122905 326.07745 114.507115 255.120828 1.35000e+02 290.28610 145.799112
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet
TSPAN6 2.371241e+01 1.052681e+01 3.406774 12.637171 9.319524 11.66387 1.096997e-08
DPM1 9.673412e+01 2.623339e+01 25.349363 57.441703 126.398809 96.63747 4.529885e+00
SCYL3 4.690892e+00 1.666745e+00 4.757625 14.125033 38.967553 39.03415 9.711817e+00
C1orf112 4.826867e-08 5.746872e-09 3.501855 3.483773 67.312927 22.59397 1.120330e+01
FGR 4.532910e+02 7.926169e+01 377.025562 550.861738 5221.426945 2573.96901 1.422560e+02
X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet
TSPAN6 2.875861e-08 0.1936674 2.579001 8.535129 4.507976 2.08324e-08 8.543531
DPM1 7.254426e+00 16.2454380 132.153918 172.153560 55.544525 2.00000e+00 70.644278
SCYL3 2.037771e+01 2.6326581 28.059641 83.549056 35.318790 1.60000e+01 10.688047
C1orf112 7.876868e+00 9.3748227 33.481367 31.790611 4.503142 1.81663e-08 50.117850
FGR 1.468920e+02 926.1487316 4857.814376 3172.066535 659.901477 5.10000e+01 2646.963079
X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet
TSPAN6 12.82058 1.1471255 1.6569770 9.995259 3.448924 7.140241 9.336288
DPM1 64.75913 19.8591620 17.5234723 207.699866 43.780377 196.427235 156.897772
SCYL3 12.83694 6.5684809 7.5938708 74.710715 20.633134 49.886991 52.208521
C1orf112 20.17010 0.9299504 0.3602555 132.928000 12.301307 39.942490 14.006890
FGR 1564.52842 102.6470558 58.4005993 5557.576808 755.336231 6420.423698 3306.665933
X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 1.102062e-08 6.385374e-08 6.685444e-08 23.061782 19.745535 31.98273 26.209261
DPM1 8.000000e+00 7.089915e+01 4.534596e+01 56.754769 29.684661 130.64919 65.403295
SCYL3 1.546687e-07 1.542958e+01 1.292976e+01 24.477278 16.773816 11.70449 7.676873
C1orf112 9.610306e-09 2.042272e+01 5.734593e+00 7.248624 1.664473 16.19771 3.559902
FGR 1.560000e+02 3.421125e+03 1.410841e+03 998.043476 336.581899 3370.32390 1087.867783
23237 more rows ...
$deviance
[1] 21.91207 20.40764 23.04180 26.64643 56.79511
23237 more elements ...
$iter
[1] 20 6 17 19 10
23237 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
23237 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6 3 28 17 33 75 6 4
DPM1 177 42 57 33 153 23 159
SCYL3 61 10 7 30 24 6 16
C1orf112 71 0 9 0 6 0 23
FGR 13362 623 379 336 1662 143 3327
X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6 9 26 22 17 15 7 42
DPM1 19 218 45 356 20 0 48
SCYL3 7 38 19 37 4 1 23
C1orf112 0 37 4 75 0 0 4
FGR 57 3506 167 13368 244 64 182
X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6 30 29 5 26 16 66 27
DPM1 3 45 16 12 22 150 40
SCYL3 4 0 1 4 1 26 15
C1orf112 0 3 0 1 1 6 1
FGR 20 473 115 49 84 743 143
X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6 11 33 24 75 3 65 25
DPM1 49 100 10 48 25 54 40
SCYL3 14 40 12 12 4 16 21
C1orf112 11 6 0 6 0 6 0
FGR 88 450 103 280 135 210 187
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet X108_Hip_non.sclerotic_pellet X108_Hip_sclerotic_pellet X125_Hip_non.sclerotic_pellet X125_Hip_sclerotic_pellet X126_Hip_non.sclerotic_pellet
TSPAN6 31 7 4 11 14 6 0
DPM1 84 30 18 73 87 127 1
SCYL3 6 1 10 1 40 38 14
C1orf112 0 0 7 0 40 32 0
FGR 385 92 240 750 3629 3360 147
X126_Hip_sclerotic_pellet X129_Hip_non.sclerotic_pellet X129_Hip_sclerotic_pellet X143_Hip_non.sclerotic_pellet X143_Hip_sclerotic_pellet X145_Hip_sclerotic_pellet X146_Hip_non.sclerotic_pellet
TSPAN6 0 0 3 11 3 0 7
DPM1 12 7 196 284 18 2 53
SCYL3 12 0 47 45 52 16 8
C1orf112 16 14 18 53 1 0 36
FGR 142 989 4530 5275 219 51 1219
X146_Hip_sclerotic_pellet X150_Hip_non.sclerotic_pellet X150_Hip_sclerotic_pellet X152_Hip_non.sclerotic_pellet X152_Hip_sclerotic_pellet X153_Hip_non.sclerotic_pellet X153_Hip_sclerotic_pellet
TSPAN6 15 0 3 11 3 5 12
DPM1 81 26 12 247 35 215 142
SCYL3 16 0 15 70 22 52 50
C1orf112 26 0 1 65 19 29 18
FGR 2410 142 35 3946 976 4738 4174
X154_Hip_sclerotic_pellet X157_Hip_non.sclerotic_pellet X157_Hip_sclerotic_pellet X158_Hip_non.sclerotic_pellet X158_Hip_sclerotic_pellet X79_Hip_non.sclerotic_pellet X79_Hip_sclerotic_pellet
TSPAN6 0 0 0 17 25 25 32
DPM1 8 76 42 58 29 110 76
SCYL3 0 13 15 27 15 17 4
C1orf112 0 26 4 3 3 3 7
FGR 156 2688 1714 827 395 6258 152
23237 more rows ...
$unshrunk.coefficients
(Intercept) patientX104 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149 patientX150 patientX151
TSPAN6 -12.655461 0.5413584 -0.077895439 0.3982037 -1.016885724 -19.6057337 0.41769739 -3.1271540 0.3086184 -1.5682311 0.102580332 -19.7709554 -0.8726869 -1.33039802 0.8363645 -1.2865564 1.9446286
DPM1 -11.067168 0.1629036 0.340799622 -0.6972292 0.002152043 -1.3552261 -0.05843641 -0.2860217 0.5139964 -0.1523274 0.180681739 -2.4864845 -0.3484969 0.12302663 -0.9068720 -0.0234429 -0.3990787
SCYL3 -12.390994 -0.6104118 -0.008379744 0.2611032 0.149264946 0.7312464 -0.47020793 -0.7820142 0.2188432 0.4485453 0.042736356 0.6465996 -0.9132023 -0.81716055 -0.8704227 0.1939999 0.3945889
C1orf112 -12.585708 -0.1643834 -0.120121656 -18.6616096 0.890601912 1.0688257 -2.06224966 0.6827334 -0.4887630 -0.3230037 0.004609488 -18.6615959 0.8267629 0.08412363 -19.2504069 -1.5661927 -1.3061229
FGR -7.167301 -1.8424785 -0.859508034 -1.8376465 -0.176631052 -1.8081614 -1.63016460 -0.1426660 -0.9711248 -1.1384428 -1.237668322 -2.7088270 -0.6248528 -0.15115207 -1.6942428 -2.2806789 -2.6540272
patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX79 patientX99 groupsclerotic
TSPAN6 -1.6414777 -1.77298345 -19.7709452 0.5283110 1.8157850 -19.58298645 0.30373767 0.4256105 -0.01072564 1.5416882 -0.7804755 0.9901228 0.4652917 0.8329009 0.3737060
DPM1 -0.1957872 -0.04673070 -0.4634388 -0.1840099 0.1479809 -0.34335011 -0.38399218 -0.3108707 -0.04863269 -0.4661411 -0.2485047 -0.3762343 0.2843186 0.6505760 -0.1191538
SCYL3 0.1055679 -0.09343686 -17.1712184 -2.9092130 -0.4904809 -0.54449673 0.09883904 -0.4729498 0.04407312 0.3075194 -0.7572605 -0.1104230 -0.8043993 -1.0519419 0.1510293
C1orf112 0.8764660 -0.12104247 -18.6615768 -1.7271123 -0.7386892 -0.06942111 -0.92338063 -1.8691480 -0.18070880 -0.7071329 -19.6039048 -1.5714649 -0.2847878 -19.2493337 -0.9423475
FGR -0.8088309 -0.45965040 -0.9540453 -1.6991791 -2.1065152 -0.36675086 -1.41680207 -2.5555571 -2.62703745 -2.1193347 -2.4619727 -2.5695909 -0.3653001 -1.7047230 -0.5579999
23237 more rows ...
$df.residual
[1] 24 24 24 24 24
23237 more elements ...
$design
(Intercept) patientX104 patientX108 patientX109 patientX125 patientX126 patientX128 patientX129 patientX130 patientX143 patientX144 patientX145 patientX146 patientX148 patientX149
X102_tibia_non.sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X102_tibia_sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X104_tibia_non.sclerotic_pellet 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
X109_tibia_sclerotic_pellet 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
X128_tibia_non.sclerotic_pellet 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
patientX150 patientX151 patientX152 patientX153 patientX154 patientX155 patientX156 patientX157 patientX158 patientX159 patientX160 patientX161 patientX163 patientX164 patientX79 patientX99
X102_tibia_non.sclerotic_pellet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X102_tibia_sclerotic_pellet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X104_tibia_non.sclerotic_pellet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X109_tibia_sclerotic_pellet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X128_tibia_non.sclerotic_pellet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
groupsclerotic
X102_tibia_non.sclerotic_pellet 0
X102_tibia_sclerotic_pellet 1
X104_tibia_non.sclerotic_pellet 0
X109_tibia_sclerotic_pellet 1
X128_tibia_non.sclerotic_pellet 0
51 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 16.23968 14.92786 14.94732 15.38006 16.18425 14.34938 15.88075 13.37373 16.09074 15.04231 16.81907 14.43626 13.50071 15.04858 13.34586 15.09993 14.09704 13.68275 13.91539 16.36253 15.21449 14.76501 16.13947 14.02727
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 15.38637 14.53455 15.40776 15.27712 14.98856 13.80278 13.95912 14.89629 15.90446 15.75514 13.93309 14.52316 14.141 16.35631 16.36788 15.35583 14.36595 15.67332 15.70549 14.07928 14.07331 16.59905 15.1613 16.39419
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 16.28865 13.7292 15.67178 15.34399 15.4899 14.96094 15.65537 15.08258
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 56
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23237 more rows ...
$dispersion
[1] 0.5439410 0.2957987 0.6792627 1.1165685 0.1538170
23237 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 2.527269 3.779531 2.131560 1.253292 7.756163
23237 more elements ...
$df.residual.zeros
[1] 22 24 24 22 24
23237 more elements ...
$df.prior
[1] 27.5638438 27.5638438 27.5638438 27.5638438 0.6333009
23237 more elements ...
$var.post
[1] 1.1742461 0.9813726 1.1688355 1.2968748 2.3196803
23237 more elements ...
$var.prior
[1] 1.3165100 1.0954825 1.3506044 1.3652549 0.5467717
23237 more elements ...
$samples51 more rows ...
$genes23237 more rows ...
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.404493
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.7783497
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.113643
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.193974
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.405346 2.405346
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 0.9345237 0.6750738
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$pellets_hip_and_tibia_sclerotic_vs_non_sclerotic$boxplot_gg
$tibia_adipocytes_sclerotic_vs_non_sclerotic
$tibia_adipocytes_sclerotic_vs_non_sclerotic$name
[1] "TSA-vs-TNSA"
$tibia_adipocytes_sclerotic_vs_non_sclerotic$results
Coefficient: groupTSA
$tibia_adipocytes_sclerotic_vs_non_sclerotic$colsums_samples
$tibia_adipocytes_sclerotic_vs_non_sclerotic$normalized_matrix
X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte
TSPAN6 6.076363e+00 4.597051e+00 1.833306e+01 4.549568e+00 9.936451e+00
TNMD 0.000000e+00 0.000000e+00 7.051177e+00 1.516523e+00 9.243210e-01
DPM1 9.789696e+00 1.264189e+01 4.230706e+00 9.604643e+00 1.617562e+01
SCYL3 8.776969e+00 9.960276e+00 9.871647e+00 3.033045e+00 2.310803e+00
C1orf112 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.310803e-01
FGR 3.915878e+01 1.394439e+02 2.256377e+01 6.622148e+01 3.951472e+01
CFH 1.350303e+00 4.213963e+00 1.410235e+00 6.571598e+00 4.159445e+00
FUCA2 2.633091e+01 1.264189e+01 4.230706e+00 1.314320e+01 1.178509e+01
GCLC 2.565575e+01 2.796539e+01 5.993500e+01 9.099135e+00 3.327556e+01
NFYA 1.755394e+01 5.401534e+01 3.384565e+01 5.307829e+01 2.033506e+01
STPG1 1.080242e+01 3.830875e-01 7.051177e-01 5.560583e+00 2.772963e+00
NIPAL3 8.776969e+00 4.213963e+00 1.621771e+01 1.314320e+01 3.235124e+00
LAS1L 3.071939e+01 8.849322e+01 3.455077e+01 4.195712e+01 4.690929e+01
ENPP4 0.000000e+00 2.298525e+00 7.051177e-01 5.055075e-01 6.239167e+00
SEMA3F 4.050909e+01 8.849322e+01 4.865312e+01 3.336350e+01 1.525130e+01
ANKIB1 1.350303e+01 1.225880e+01 1.269212e+01 1.465972e+01 1.386482e+01
CYP51A1 1.654121e+01 6.895576e+00 4.935824e+00 1.162667e+01 8.781050e+00
KRIT1 6.076363e+00 1.187571e+01 1.057677e+01 1.263769e+01 9.705371e+00
RAD52 1.350303e+01 3.064700e+00 1.833306e+01 0.000000e+00 7.625648e+00
MYH16 0.000000e+00 1.915438e+00 0.000000e+00 0.000000e+00 6.932408e-01
BAD 6.211393e+01 3.141318e+01 4.371730e+01 6.419945e+01 6.955516e+01
LAP3 2.869394e+01 4.673668e+01 2.608935e+01 3.488002e+01 3.812824e+01
CD99 2.400163e+02 1.647276e+02 2.221121e+02 2.471932e+02 2.645869e+02
HS3ST1 1.451576e+01 2.451760e+01 9.166530e+00 9.604643e+00 1.086077e+01
AOC1 0.000000e+00 5.746313e+00 1.410235e+00 0.000000e+00 2.310803e-01
WNT16 1.012727e+00 1.532350e+00 1.410235e+00 0.000000e+00 6.932408e-01
HECW1 2.363030e+00 1.532350e+00 4.935824e+00 8.088120e+00 2.541883e+00
MAD1L1 1.012727e+01 6.129401e+00 3.525588e+00 1.314320e+01 5.545926e+00
LASP1 2.970666e+02 1.831158e+02 2.178814e+02 2.153462e+02 3.438474e+02
SNX11 1.181515e+01 7.278663e+00 1.621771e+01 3.538553e+00 5.777006e+00
TMEM176A 2.329272e+01 3.332862e+01 9.871647e+00 4.448466e+01 2.703639e+01
X109_tibia_sclerotic_adipocyte X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte
TSPAN6 1.025967e+01 7.166957e+00 4.700622e+00 7.881550e+00 3.006245
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000
DPM1 1.413555e+01 1.522978e+01 5.640747e+00 1.069639e+01 13.027061
SCYL3 2.963905e+00 1.791739e+00 4.700622e+00 2.251871e+00 0.000000
C1orf112 5.015839e+00 0.000000e+00 0.000000e+00 5.629678e-01 0.000000
FGR 8.321732e+01 3.762652e+01 3.290435e+01 2.277205e+02 200.416325
CFH 5.243831e+00 1.791739e+00 0.000000e+00 1.125936e+00 4.008327
FUCA2 1.778343e+01 2.015707e+01 1.598212e+01 1.125936e+01 12.024980
GCLC 3.579485e+01 2.687609e+01 3.666485e+01 3.771885e+01 26.054122
NFYA 1.846741e+01 1.657359e+01 5.452722e+01 2.758542e+01 17.035388
STPG1 6.383795e+00 1.791739e+00 2.820373e+00 7.037098e+00 0.000000
NIPAL3 8.207736e+00 1.254217e+01 8.461120e+00 1.801497e+01 4.008327
LAS1L 4.901842e+01 3.538685e+01 3.290435e+01 2.955581e+01 11.022898
ENPP4 1.823941e+00 2.239674e+00 3.760498e+00 1.463716e+01 4.008327
SEMA3F 2.576317e+01 2.015707e+01 2.068274e+01 4.250407e+01 15.031224
ANKIB1 1.003168e+01 1.433391e+01 3.196423e+01 1.238529e+01 16.033306
CYP51A1 1.732744e+01 2.239674e+01 1.222162e+01 8.163034e+00 3.006245
KRIT1 9.347699e+00 1.881326e+01 9.401244e+00 1.013342e+01 7.014571
RAD52 9.575692e+00 1.612565e+01 1.880249e+00 9.007486e+00 7.014571
MYH16 1.367956e+00 0.000000e+00 2.820373e+00 5.629678e-01 0.000000
BAD 5.608620e+01 7.256544e+01 4.230560e+01 2.420762e+01 31.064530
LAP3 3.898675e+01 2.060500e+01 4.794635e+01 4.053368e+01 28.058286
CD99 2.991264e+02 3.171378e+02 2.209292e+02 1.531273e+02 256.532897
HS3ST1 1.413555e+01 8.958696e+00 0.000000e+00 1.773349e+01 8.016653
AOC1 1.139963e+00 0.000000e+00 0.000000e+00 1.970387e+00 0.000000
WNT16 0.000000e+00 8.958696e-01 0.000000e+00 2.814839e-01 0.000000
HECW1 6.383795e+00 8.958696e+00 0.000000e+00 5.629678e-01 0.000000
MAD1L1 5.699817e+00 5.375218e+00 2.820373e+00 1.435568e+01 7.014571
LASP1 3.374291e+02 3.973182e+02 3.854510e+02 3.445363e+02 224.466284
SNX11 8.435729e+00 1.478185e+01 9.401244e+00 5.066711e+00 14.029143
TMEM176A 6.064605e+01 2.777196e+01 2.444324e+01 2.280020e+01 40.083265
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte
TSPAN6 4.702029e+00 7.378439e+00 5.467025e+00 1.025351e+01 1.271424e+01
TNMD 7.233891e-02 0.000000e+00 4.970022e-01 0.000000e+00 2.801442e+00
DPM1 1.258697e+01 1.249574e+01 1.673241e+01 2.343658e+01 1.422271e+01
SCYL3 3.616946e+00 3.689220e+00 2.982013e+00 2.929573e+00 2.585946e+00
C1orf112 1.157423e+00 1.666099e+00 3.147681e+00 0.000000e+00 0.000000e+00
FGR 2.311228e+02 1.122237e+02 2.489981e+02 4.599430e+02 5.258091e+01
CFH 1.808473e+00 2.618156e+00 3.313348e-01 0.000000e+00 5.602884e+00
FUCA2 1.548053e+01 1.630397e+01 1.606974e+01 4.394360e+00 1.702415e+01
GCLC 4.694795e+01 3.046581e+01 7.372200e+01 1.230421e+02 3.447929e+01
NFYA 3.125041e+01 2.725262e+01 4.323920e+01 5.859146e+01 3.124685e+01
STPG1 7.523247e+00 1.904113e+00 9.111708e+00 8.788719e+00 5.171893e+00
NIPAL3 1.540819e+01 6.664397e+00 1.491007e+01 5.859146e+00 8.835317e+00
LAS1L 3.624180e+01 3.510709e+01 3.710950e+01 2.197180e+01 3.469478e+01
ENPP4 2.748879e+00 3.451205e+00 4.638688e+00 4.394360e+00 1.228325e+01
SEMA3F 2.539096e+01 1.463787e+01 4.837489e+01 1.757744e+01 2.736793e+01
ANKIB1 1.215294e+01 1.547092e+01 1.673241e+01 0.000000e+00 1.357622e+01
CYP51A1 9.765753e+00 1.142468e+01 1.474440e+01 1.464787e+00 1.142126e+01
KRIT1 1.454012e+01 1.106766e+01 6.792364e+00 0.000000e+00 6.680362e+00
RAD52 5.570096e+00 4.522269e+00 7.786369e+00 2.929573e+00 3.232433e+00
MYH16 0.000000e+00 2.380142e-01 8.283371e-01 0.000000e+00 0.000000e+00
BAD 4.123318e+01 4.974496e+01 4.688388e+01 1.318308e+01 5.236541e+01
LAP3 3.559075e+01 3.332198e+01 3.677817e+01 2.197180e+01 4.159064e+01
CD99 1.673922e+02 1.988608e+02 1.353503e+02 1.274364e+02 2.646285e+02
HS3ST1 1.063382e+01 1.392383e+01 9.111708e+00 1.025351e+01 7.757839e+00
AOC1 5.714774e+00 2.380142e-01 4.970022e+00 0.000000e+00 8.188830e+00
WNT16 1.012745e+00 4.760283e-01 6.626697e-01 0.000000e+00 8.619821e-01
HECW1 1.663795e+00 4.998298e+00 1.656674e+00 0.000000e+00 9.050812e+00
MAD1L1 9.187042e+00 1.487589e+01 8.614706e+00 0.000000e+00 7.326848e+00
LASP1 3.673370e+02 3.554742e+02 3.134428e+02 2.021405e+02 3.366040e+02
SNX11 1.859110e+01 1.273376e+01 1.590407e+01 1.171829e+01 1.099027e+01
TMEM176A 5.324144e+01 6.723900e+01 4.439887e+01 5.859146e+00 3.663424e+01
X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte
TSPAN6 1.135028e+01 1.810273e+00 0.000000e+00 5.145781e+00 7.277910e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.286593e+00 1.176677e+01 2.649445e+01 1.148826e+01 1.273634e+01
SCYL3 7.222905e+00 4.978251e+00 0.000000e+00 2.513056e+00 4.548694e-01
C1orf112 6.878957e-01 0.000000e+00 0.000000e+00 3.590080e-01 0.000000e+00
FGR 5.262402e+01 3.258491e+01 1.519015e+02 5.636426e+01 5.276484e+01
CFH 4.471322e+00 5.430819e+00 8.831484e+00 2.154048e+00 5.913302e+00
FUCA2 1.582160e+01 2.851180e+01 1.413037e+01 1.376197e+01 2.592755e+01
GCLC 1.685345e+01 2.851180e+01 2.296186e+01 3.637948e+01 9.552256e+00
NFYA 3.645847e+01 1.493475e+01 0.000000e+00 2.249783e+01 2.865677e+01
STPG1 7.910801e+00 1.221934e+01 0.000000e+00 5.744128e+00 2.729216e+00
NIPAL3 1.238212e+01 4.978251e+00 1.766297e+01 1.160793e+01 7.277910e+00
LAS1L 2.682793e+01 3.620546e+01 1.766297e+01 4.451699e+01 4.594180e+01
ENPP4 4.815270e+00 1.629246e+01 0.000000e+00 6.940821e+00 6.368171e+00
SEMA3F 3.370689e+01 1.855530e+01 2.472816e+01 1.579635e+01 1.410095e+01
ANKIB1 1.410186e+01 2.081814e+01 1.413037e+01 1.926676e+01 7.732779e+00
CYP51A1 1.169423e+01 1.810273e+00 4.415742e+01 8.137515e+00 1.637530e+01
KRIT1 1.341397e+01 9.956502e+00 1.942927e+01 1.340297e+01 1.228147e+01
RAD52 1.272607e+01 1.040907e+01 3.355964e+01 8.017845e+00 1.319121e+01
MYH16 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
BAD 5.950298e+01 5.068764e+01 3.709223e+01 5.181682e+01 2.820190e+01
LAP3 2.338846e+01 4.344655e+01 4.769002e+01 4.355964e+01 6.550119e+01
CD99 2.414514e+02 2.086340e+02 1.713308e+02 2.198326e+02 1.983230e+02
HS3ST1 8.598697e+00 7.241092e+00 2.826075e+01 6.940821e+00 1.501069e+01
AOC1 8.942645e+00 0.000000e+00 0.000000e+00 7.180160e-01 0.000000e+00
WNT16 0.000000e+00 0.000000e+00 0.000000e+00 7.180160e-01 4.548694e-01
HECW1 1.238212e+01 4.073114e+00 1.766297e+00 1.914709e+00 5.003563e+00
MAD1L1 5.159218e+00 5.430819e+00 2.119556e+01 8.616192e+00 9.097387e+00
LASP1 3.755911e+02 2.656576e+02 3.426616e+02 3.999349e+02 3.270511e+02
SNX11 4.815270e+00 4.978251e+00 2.119556e+01 1.041123e+01 1.683017e+01
TMEM176A 2.614004e+01 3.756316e+01 4.239112e+01 2.632725e+01 8.369596e+01
X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte X160_Tibia_non.sclerotic_adipocyte
TSPAN6 9.450250e+00 2.491723e+00 9.861323e+00 8.888556e+00 1.136393e+01
TNMD 1.512040e+00 0.000000e+00 1.195312e+00 1.437855e+00 1.010127e+00
DPM1 7.434197e+00 9.254973e+00 1.180370e+01 1.111069e+01 1.304748e+01
SCYL3 4.788127e+00 1.779802e+00 5.378903e+00 3.921422e-01 2.272787e+00
C1orf112 1.260033e+00 0.000000e+00 2.988280e-01 2.614281e-01 6.734183e-01
FGR 3.704498e+01 2.598512e+01 1.942382e+01 2.862638e+01 1.414178e+01
CFH 5.040134e-01 1.067881e+00 2.091796e+00 2.091425e+00 2.188609e+00
FUCA2 1.751446e+01 7.475170e+00 1.688378e+01 1.908425e+01 1.641457e+01
GCLC 3.187884e+01 2.634108e+01 3.346873e+01 4.261278e+01 3.737472e+01
NFYA 4.611722e+01 2.527319e+01 2.794041e+01 3.150209e+01 3.274496e+01
STPG1 9.450250e+00 1.423842e+00 3.735350e+00 5.882132e+00 8.249374e+00
NIPAL3 2.381463e+01 8.543052e+00 8.666011e+00 1.084927e+01 9.764565e+00
LAS1L 3.742299e+01 5.019043e+01 3.959470e+01 4.143635e+01 3.686965e+01
ENPP4 7.560200e+00 3.559605e+00 6.723629e+00 4.052136e+00 6.060765e+00
SEMA3F 3.313888e+01 3.203644e+01 2.689452e+01 1.869211e+01 2.104432e+01
ANKIB1 2.457065e+01 1.530630e+01 2.569920e+01 1.751568e+01 2.584243e+01
CYP51A1 8.568227e+00 1.495034e+01 1.120605e+01 2.705781e+01 1.481520e+01
KRIT1 8.694230e+00 2.242551e+01 1.882616e+01 1.516283e+01 8.586083e+00
RAD52 7.056187e+00 1.495034e+01 1.210253e+01 6.274275e+00 1.094305e+01
MYH16 0.000000e+00 0.000000e+00 0.000000e+00 1.307141e+00 0.000000e+00
BAD 4.107709e+01 6.514077e+01 6.439743e+01 4.980205e+01 5.833486e+01
LAP3 5.682751e+01 4.129142e+01 3.989353e+01 4.457349e+01 3.358674e+01
CD99 2.489826e+02 3.118214e+02 2.435448e+02 2.509710e+02 2.438616e+02
HS3ST1 1.083629e+01 1.673014e+01 1.479198e+01 9.542126e+00 1.010127e+01
AOC1 1.260033e+00 1.067881e+00 5.976559e-01 5.228562e-01 0.000000e+00
WNT16 6.300167e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
HECW1 6.300167e+00 3.203644e+00 7.470699e+00 1.437855e+01 8.754438e+00
MAD1L1 7.434197e+00 7.831131e+00 6.873043e+00 3.921422e+00 7.491779e+00
LASP1 3.763720e+02 2.762253e+02 3.133211e+02 3.635158e+02 4.629751e+02
SNX11 9.828260e+00 1.210266e+01 1.299902e+01 8.888556e+00 8.754438e+00
TMEM176A 2.772073e+01 2.883280e+01 1.733202e+01 2.222139e+01 1.734052e+01
X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6 8.849039e+00 7.814302e+00 6.966786e+00 9.673851 1.992373e+00
TNMD 3.356532e+00 9.494012e-01 0.000000e+00 0.000000 0.000000e+00
DPM1 1.271414e+01 1.942621e+01 8.866819e+00 13.088151 3.320622e+00
SCYL3 3.356532e+00 3.213358e+00 2.406708e+00 10.811951 3.984746e+00
C1orf112 8.137048e-01 6.572778e-01 1.140020e+00 0.000000 0.000000e+00
FGR 2.115632e+01 4.265002e+01 4.541078e+01 25.607251 1.338211e+02
CFH 3.865098e+00 2.190926e+00 1.646695e+00 1.138100 1.328249e+00
FUCA2 1.566382e+01 1.124675e+01 1.152686e+01 15.933401 3.353828e+01
GCLC 3.407389e+01 2.621808e+01 2.780381e+01 22.192951 2.058785e+01
NFYA 3.509102e+01 4.089728e+01 2.989385e+01 13.088151 1.494280e+01
STPG1 8.340474e+00 4.747006e+00 4.433410e+00 7.397650 6.641243e+00
NIPAL3 1.047645e+01 1.205009e+01 1.342690e+01 5.690500 1.527486e+01
LAS1L 4.261779e+01 3.914454e+01 2.704380e+01 26.745352 4.383221e+01
ENPP4 3.051393e+00 5.258222e+00 4.306741e+00 3.414300 2.656497e+00
SEMA3F 2.756425e+01 3.395935e+01 3.407392e+01 11.381001 2.689704e+01
ANKIB1 1.627410e+01 1.833075e+01 1.634028e+01 5.121450 1.627105e+01
CYP51A1 1.739294e+01 1.453314e+01 1.399691e+01 3.414300 1.029393e+01
KRIT1 1.800322e+01 1.095463e+01 1.209687e+01 15.364351 1.095805e+01
RAD52 1.108673e+01 1.168494e+01 1.064018e+01 2.276200 1.062599e+01
MYH16 0.000000e+00 3.651543e-01 8.866819e-01 2.276200 0.000000e+00
BAD 4.627946e+01 4.520610e+01 4.211739e+01 57.474053 4.183983e+01
LAP3 3.824412e+01 4.367246e+01 4.281407e+01 17.640551 3.586271e+01
CD99 2.718791e+02 1.852063e+02 1.983634e+02 207.703262 2.782681e+02
HS3ST1 8.747326e+00 1.161191e+01 1.165353e+01 6.828600 1.527486e+01
AOC1 0.000000e+00 4.381852e-01 1.140020e+00 0.000000 3.320622e-01
WNT16 7.119917e-01 2.190926e-01 0.000000e+00 0.000000 7.305368e+00
HECW1 1.108673e+01 7.449148e+00 4.116737e+00 1.707150 0.000000e+00
MAD1L1 8.849039e+00 5.185191e+00 8.676816e+00 2.845250 8.301554e+00
LASP1 3.641329e+02 3.119878e+02 3.380791e+02 476.294877 3.181156e+02
SNX11 5.289081e+00 6.134592e+00 6.650114e+00 6.259550 2.490466e+01
TMEM176A 5.319595e+01 2.614505e+01 5.953436e+01 11.950051 2.424054e+01
X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte
TSPAN6 2.352198e+01 1.358506e+00
TNMD 0.000000e+00 0.000000e+00
DPM1 1.447507e+01 8.490665e+00
SCYL3 4.975804e+00 0.000000e+00
C1orf112 4.523458e-01 0.000000e+00
FGR 2.397433e+01 1.005295e+02
CFH 4.523458e+00 2.377386e+00
FUCA2 1.311803e+01 1.154730e+01
GCLC 1.492741e+01 3.158527e+01
NFYA 2.080791e+01 3.498154e+01
STPG1 9.499262e+00 6.792532e-01
NIPAL3 1.673679e+01 1.596245e+01
LAS1L 3.166421e+01 4.618922e+01
ENPP4 2.261729e+00 7.811412e+00
SEMA3F 2.714075e+00 2.071722e+01
ANKIB1 2.804544e+01 1.698133e+01
CYP51A1 4.975804e+00 1.596245e+01
KRIT1 1.899852e+01 7.471785e+00
RAD52 9.046916e-01 3.735893e+00
MYH16 0.000000e+00 0.000000e+00
BAD 8.096990e+01 4.245333e+01
LAP3 3.935409e+01 3.260415e+01
CD99 2.505996e+02 2.224554e+02
HS3ST1 8.594570e+00 2.717013e+01
AOC1 0.000000e+00 0.000000e+00
WNT16 1.809383e+00 2.717013e+00
HECW1 9.499262e+00 5.434026e+00
MAD1L1 6.332841e+00 1.052842e+01
LASP1 3.772564e+02 2.784938e+02
SNX11 5.428150e+00 8.830292e+00
TMEM176A 1.990322e+01 2.343424e+01
[ reached getOption("max.print") -- omitted 23227 rows ]
$tibia_adipocytes_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) batchX104 batchX105 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99
TSPAN6 -11.66177 -0.62295592 0.36522127 0.3489849 -0.21180216 -0.2860687 -0.1346908 0.02424395 0.5101485 -1.80082953 -0.1420072 -0.2424379 0.2648817 0.3274959 0.02708262 -0.32928163 1.0052453 -1.82929541
TNMD -15.81852 -1.69556791 4.04261334 1.5869947 -1.36440513 -1.4717734 -0.2452323 1.27982699 2.5776436 -1.49814352 -1.4504825 2.0734943 3.4991815 4.2641287 1.50009573 -0.93534616 -1.6955679 -1.69556791
DPM1 -11.43940 0.16286130 -0.35888522 0.3880371 0.03714267 0.1324860 0.2014723 0.64959355 0.1324769 0.57782325 0.1633210 -0.2093787 0.1104829 0.2279832 0.30478983 -0.27635455 0.2980255 -0.23423198
SCYL3 -11.12108 -0.39334493 -0.67199147 -1.4048301 -1.22853414 -2.2241578 -1.1030944 -1.40657102 -0.7234495 -1.45998083 -2.0655106 -1.3049623 -1.5628729 -1.3192803 -1.39720638 -0.52120525 -1.0848820 -6.39301023
C1orf112 -17.45450 -0.05958904 -0.02555592 4.6687069 -0.04015864 2.7046401 4.0344145 4.27487472 2.6122500 -0.04712352 2.2608111 3.3021214 2.4793114 3.4073225 3.59787960 -0.02292444 2.8989691 -0.05958904
groupTSA
TSPAN6 -0.34526954
TNMD -1.69556791
DPM1 -0.09225483
SCYL3 -0.51948440
C1orf112 -0.05958904
23253 more rows ...
$fitted.values
X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6 1.800000e+01 1.200000e+01 1.757325e+01 1.733060e+01 52.778484 37.820425
TNMD 1.158125e-08 1.020338e-08 1.350688e+01 2.275058e+00 2.806181 0.343448
DPM1 2.900000e+01 3.300000e+01 1.062668e+01 1.351289e+01 68.554845 63.342685
SCYL3 2.600000e+01 2.600000e+01 1.069219e+01 8.820703e+00 15.628570 9.368367
C1orf112 2.594062e-08 2.284082e-08 1.323546e-08 1.728447e-08 12.077075 11.460054
X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6 1.550983e+01 5.224733e+00 2.290853e+01 4.549621e+00 103.7951316 44.60706843
TNMD 1.537838e-08 8.847967e-10 2.264966e-08 7.682731e-10 0.8652398 0.06350955
DPM1 2.488324e+01 1.080819e+01 4.356602e+01 1.115616e+01 181.6611231 100.66477252
SCYL3 9.629576e+00 2.713559e+00 5.597135e+00 9.298630e-01 67.6598688 24.32388791
C1orf112 2.002831e-08 8.934220e-09 1.316152e+00 3.461303e-01 20.2504100 11.52433684
X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6 53.142827 4.24947175 66.513180 29.4632668 3.089862e+00 5.597409e-01
TNMD 2.807634 0.03834481 8.473526 0.6410814 1.317628e-08 4.076775e-10
DPM1 124.254754 12.81126831 56.906651 32.5031188 4.233013e+01 9.887496e+00
SCYL3 21.737053 1.45400569 33.303165 12.3405306 7.542126e+00 1.142923e+00
C1orf112 11.273342 1.19370876 1.543938 0.9056463 1.949677e-08 4.676985e-09
X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6 6.227506e+01 1.158345e+01 53.459220 13.3792082 75.022863 60.630357
TNMD 5.753792e-08 1.827906e-09 8.638478 0.3692503 42.219560 5.827551
DPM1 1.056929e+02 2.534886e+01 69.084438 22.2934276 80.286750 83.662183
SCYL3 1.545144e+01 2.404185e+00 31.658488 6.6278567 20.549605 13.892331
C1orf112 1.918051e+00 4.724319e-01 5.481824 1.8167214 1.933889 2.069586
X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6 141.785495 82.961651 120.918370 98.579460 1.084580e+01 1.314075e+01
TNMD 168.374808 16.826685 7.755859 1.079941 1.660587e-08 3.436340e-09
DPM1 160.315251 120.950939 199.554207 209.770233 1.430145e+01 2.234228e+01
SCYL3 46.784009 22.899087 49.807517 33.967547 1.541718e+01 1.562567e+01
C1orf112 9.151423 7.090709 12.843483 13.865400 1.648242e-08 2.644448e-08
X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte
TSPAN6 5.200000e+01 4.000000e+00
TNMD 8.641161e-09 1.150906e-08
DPM1 3.200000e+01 2.500000e+01
SCYL3 1.100000e+01 1.681699e-07
C1orf112 1.000000e+00 2.576369e-08
23253 more rows ...
$deviance
[1] 9.772060 8.017749 9.392321 13.662324 9.226843
23253 more elements ...
$iter
[1] 7 19 6 18 18
23253 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
23253 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_sclerotic_adipocyte X104_tibia_non.sclerotic_adipocyte X105_tibia_non.sclerotic_adipocyte X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte
TSPAN6 18 12 26 9 43 45
TNMD 0 0 10 3 4 0
DPM1 29 33 6 19 70 62
SCYL3 26 26 14 6 10 13
C1orf112 0 0 0 0 1 22
X128_tibia_non.sclerotic_adipocyte X128_tibia_sclerotic_adipocyte X130_Tibia_non.sclerotic_adipocyte X130_Tibia_sclerotic_adipocyte X144_Tibia_non.sclerotic_adipocyte X144_Tibia_sclerotic_adipocyte
TSPAN6 16 5 28 3 65 62
TNMD 0 0 0 0 1 0
DPM1 34 6 38 13 174 105
SCYL3 4 5 8 0 50 31
C1orf112 0 0 2 0 16 14
X148_Tibia_non.sclerotic_adipocyte X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_sclerotic_adipocyte X151_Tibia_non.sclerotic_adipocyte X151_Tibia_sclerotic_adipocyte
TSPAN6 33 7 59 33 4 0
TNMD 3 0 13 0 0 0
DPM1 101 16 66 27 26 15
SCYL3 18 2 12 21 11 0
C1orf112 19 0 0 2 0 0
X155_Tibia_non.sclerotic_adipocyte X155_Tibia_sclerotic_adipocyte X156_Tibia_non.sclerotic_adipocyte X156_Tibia_sclerotic_adipocyte X159_Tibia_non.sclerotic_adipocyte X159_Tibia_sclerotic_adipocyte
TSPAN6 43 16 75 7 66 68
TNMD 0 0 12 0 8 11
DPM1 96 28 59 26 79 85
SCYL3 21 1 38 5 36 3
C1orf112 3 0 10 0 2 2
X160_Tibia_non.sclerotic_adipocyte X160_Tibia_sclerotic_adipocyte X161_Tibia_non.sclerotic_adipocyte X161_Tibia_sclerotic_adipocyte X163_Tibia_non.sclerotic_adipocyte X163_Tibia_sclerotic_adipocyte
TSPAN6 135 87 107 110 17 6
TNMD 12 33 13 0 0 0
DPM1 155 125 266 140 23 10
SCYL3 27 33 44 38 19 12
C1orf112 8 8 9 18 0 0
X164_tibia_non.sclerotic_adipocyte X99_Tibia_non.sclerotic_adipocyte
TSPAN6 52 4
TNMD 0 0
DPM1 32 25
SCYL3 11 0
C1orf112 1 0
23253 more rows ...
$unshrunk.coefficients
(Intercept) batchX104 batchX105 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99
TSPAN6 -11.66440 -0.62569730 0.365874987 0.3500012 -0.21274568 -0.287283 -0.1350862 0.02409791 0.5114728 -1.81580236 -0.1425740 -0.243640 0.2656463 0.3283730 0.02713032 -0.331121234 1.0068232 -1.84472633
TNMD -31.06136 -2.11419066 19.499657010 16.8126824 -1.54756253 -1.624953 14.4747065 16.48041730 17.8479798 -1.69181576 -1.5479963 17.330628 19.0876974 19.8972105 16.67742364 -1.231448112 -2.1141891 -2.11419165
DPM1 -11.44165 0.16315920 -0.359879003 0.3887872 0.03723045 0.132741 0.2018933 0.65070428 0.1327405 0.57882577 0.1636583 -0.209974 0.1107135 0.2284554 0.30535613 -0.277282786 0.2985709 -0.23488928
SCYL3 -11.11817 -0.39873977 -0.677221939 -1.4132341 -1.23561293 -2.242770 -1.1092444 -1.41609926 -0.7265072 -1.46965720 -2.0826652 -1.313785 -1.5755373 -1.3266333 -1.40605181 -0.525649128 -1.0927576 -19.37554397
C1orf112 -32.30304 -0.06668053 -0.002228838 19.5138467 -0.04169894 17.494560 18.8693098 19.11219566 17.3870494 -0.05830585 17.0158144 18.117519 17.2460263 18.2266072 18.42349128 0.002769465 17.6942196 -0.06668022
groupTSA
TSPAN6 -0.34670591
TNMD -2.11399556
DPM1 -0.09252625
SCYL3 -0.52521349
C1orf112 -0.06589317
23253 more rows ...
$df.residual
[1] 13 13 13 13 13
23253 more elements ...
$design
(Intercept) batchX104 batchX105 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99
X102_tibia_sclerotic_adipocyte 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X104_tibia_non.sclerotic_adipocyte 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X105_tibia_non.sclerotic_adipocyte 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X105_tibia_sclerotic_adipocyte 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X109_tibia_non.sclerotic_adipocyte 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
groupTSA
X102_tibia_sclerotic_adipocyte 1
X104_tibia_non.sclerotic_adipocyte 0
X105_tibia_non.sclerotic_adipocyte 0
X105_tibia_sclerotic_adipocyte 1
X109_tibia_non.sclerotic_adipocyte 0
27 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 14.90148 14.775 14.1649 14.4977 15.2805 15.29395 14.61862 13.87725 15.08319 13.81343 16.4419 15.94408 15.61328 13.4338 15.35033 14.88278 14.60833 13.24663 15.93853 14.60326 15.88696 14.84845 15.71654 15.85025 16.29034
[,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 16.10111 16.43238 16.57484 14.3793 14.91794 14.60882 14.89542
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 32
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
23253 more rows ...
$dispersion
[1] 0.2872179 1.5359262 0.2041911 0.4959211 1.5430748
23253 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 3.022363 0.176057 3.656305 2.044776 0.169501
23253 more elements ...
$df.residual.zeros
[1] 13 8 13 13 9
23253 more elements ...
$df.prior
[1] 159.471 159.471 159.471 159.471 159.471
23253 more elements ...
$var.post
[1] 1.244144 1.361507 1.149438 1.355407 1.360682
23253 more elements ...
$var.prior
[1] 1.284288 1.379531 1.184243 1.380226 1.379615
23253 more elements ...
$samples27 more rows ...
$genes23253 more rows ...
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.8391389
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.8601605
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 1.394509
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 1.443521
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 1.699138 1.699138
$tibia_adipocytes_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 1.1568013 0.8700811
$tibia_adipocytes_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$tibia_adipocytes_sclerotic_vs_non_sclerotic$boxplot_gg
$tibia_pellet_sclerotic_vs_non_sclerotic
$tibia_pellet_sclerotic_vs_non_sclerotic$name
[1] "TSP-vs-TNSP"
$tibia_pellet_sclerotic_vs_non_sclerotic$results
Coefficient: groupTSP
$tibia_pellet_sclerotic_vs_non_sclerotic$colsums_samples
$tibia_pellet_sclerotic_vs_non_sclerotic$normalized_matrix
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet
TSPAN6 2.369877e-01 8.947041e+00 5.291329e+00 6.836571e+00 7.008758e+00 3.420468
DPM1 1.398228e+01 1.342056e+01 1.774152e+01 6.836571e+00 1.429787e+01 13.111794
SCYL3 4.818750e+00 3.195372e+00 2.178783e+00 6.215065e+00 2.242803e+00 3.420468
C1orf112 5.608709e+00 0.000000e+00 2.801292e+00 0.000000e+00 5.607006e-01 0.000000
FGR 1.055543e+03 1.990717e+02 1.179655e+02 6.960872e+01 1.553141e+02 81.521152
CFH 7.109631e-01 3.514909e+00 1.556273e+00 2.486026e+00 6.541507e-01 3.990546
FUCA2 1.090143e+01 1.853316e+01 5.913839e+00 1.719501e+01 1.055986e+01 19.952730
GCLC 4.565963e+01 1.917223e+01 1.649650e+01 1.035844e+01 2.691363e+01 5.130702
NFYA 5.379621e+01 3.419048e+01 3.859558e+01 3.148966e+01 3.261409e+01 38.195225
STPG1 2.053894e+00 6.071206e+00 3.423801e+00 8.286753e-01 4.859406e+00 15.392106
NIPAL3 1.658914e+01 1.022519e+01 4.980075e+00 1.222296e+01 1.654067e+01 27.933821
LAS1L 4.700256e+01 3.674677e+01 7.189983e+01 2.216706e+01 4.831370e+01 22.803119
ENPP4 1.224437e+01 4.473520e+00 3.112547e+00 3.314701e+00 7.943259e+00 3.420468
SEMA3F 1.342930e+00 2.204806e+01 7.501237e+01 5.179220e+01 5.719147e+01 31.354289
ANKIB1 7.188627e+00 1.342056e+01 1.245019e+01 1.056561e+01 1.654067e+01 9.691326
CYP51A1 6.082685e+00 7.988429e+00 1.276144e+01 8.701090e+00 6.915308e+00 10.261404
KRIT1 1.019047e+01 9.266578e+00 1.649650e+01 1.636634e+01 1.644722e+01 9.121248
RAD52 1.153340e+01 1.917223e+00 7.470112e+00 1.367314e+01 1.055986e+01 3.990546
MYH16 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.869002e-01 0.000000
BAD 2.172387e+01 5.336271e+01 2.241034e+01 3.874057e+01 2.794158e+01 36.484991
LAP3 1.516721e+01 1.469871e+01 3.361550e+01 2.361725e+01 3.709969e+01 46.746395
CD99 7.315021e+01 1.907637e+02 1.494022e+02 3.530157e+02 2.032540e+02 280.478370
HS3ST1 1.421926e+00 1.853316e+01 1.462897e+01 3.874057e+01 2.859573e+01 36.484991
AOC1 4.344775e+00 4.473520e+00 6.225093e-01 4.143376e-01 1.682102e+00 0.570078
WNT16 7.899590e-02 1.310102e+01 0.000000e+00 4.143376e-01 1.401752e+00 29.073977
HECW1 6.319672e-01 2.556297e+00 4.980075e+00 4.143376e+00 1.495202e+00 4.560624
MAD1L1 2.022295e+01 1.885269e+01 5.913839e+00 9.322597e+00 1.233541e+01 5.700780
LASP1 2.978146e+02 2.083382e+02 1.715013e+02 3.030880e+02 2.433441e+02 145.939965
SNX11 6.240676e+00 3.514909e+00 4.046311e+00 7.043740e+00 8.690860e+00 7.411014
TMEM176A 3.080840e+00 6.710281e+00 1.338395e+01 4.329828e+01 1.850312e+01 15.962184
M6PR 4.044590e+01 2.204806e+01 2.645665e+01 2.403158e+01 2.420358e+01 24.513353
KLHL13 7.899590e-01 8.627504e+00 9.337640e-01 4.143376e-01 1.027951e+00 1.140156
CYP26B1 2.527869e+00 4.313752e+01 1.092504e+02 4.557714e+01 1.831622e+01 45.036161
X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet
TSPAN6 4.773253e-01 1.249578e+01 2.506446e+00 6.273754e+00 7.801261e-01 7.871938e+00
DPM1 1.897368e+01 2.637997e+01 2.101558e+01 1.283268e+01 1.633676e+01 1.049592e+01
SCYL3 1.909301e+00 9.718936e+00 3.663267e+00 5.418242e+00 1.697921e+00 2.099183e+00
C1orf112 2.744620e+00 0.000000e+00 3.566865e+00 1.140683e+00 3.441733e+00 0.000000e+00
FGR 3.970153e+02 7.913991e+01 3.379846e+02 4.762350e+01 6.134544e+02 1.280502e+02
CFH 7.159879e-01 5.553678e+00 3.856071e-01 4.562730e+00 2.753386e-01 7.347142e+00
FUCA2 1.169447e+01 2.776839e+00 1.773792e+01 4.847901e+00 9.177954e+00 6.297550e+00
GCLC 6.026232e+01 2.637997e+01 4.685126e+01 7.129266e+00 9.659796e+01 1.469428e+01
NFYA 3.639605e+01 2.499155e+01 3.672907e+01 2.623570e+01 4.928561e+01 5.772754e+00
STPG1 3.699271e+00 1.249578e+01 4.338079e+00 1.711024e+00 4.497197e+00 2.099183e+00
NIPAL3 1.718371e+01 1.666103e+01 1.754512e+01 2.081746e+01 1.808057e+01 8.396734e+00
LAS1L 3.818602e+01 3.609891e+01 4.579084e+01 3.992389e+01 5.571018e+01 3.096295e+01
ENPP4 5.727903e+00 4.165258e+00 7.615739e+00 3.422048e+00 2.891055e+00 2.099183e+00
SEMA3F 2.852019e+01 1.804945e+01 9.061766e+00 3.479082e+01 9.545072e+00 3.096295e+01
ANKIB1 9.904500e+00 1.110736e+01 6.940927e+00 2.338399e+01 7.893040e+00 6.297550e+00
CYP51A1 7.398542e+00 0.000000e+00 4.916490e+00 9.410631e+00 7.525922e+00 7.871938e+00
KRIT1 9.665837e+00 2.776839e+00 1.301424e+01 1.112165e+01 1.693332e+01 1.416949e+01
RAD52 1.073982e+01 1.249578e+01 1.262863e+01 5.133072e+00 1.330803e+01 9.971121e+00
MYH16 0.000000e+00 0.000000e+00 0.000000e+00 2.566536e+00 9.177954e-02 0.000000e+00
BAD 3.031016e+01 2.221471e+01 2.275082e+01 4.819384e+01 2.097162e+01 5.510356e+01
LAP3 3.198079e+01 1.943787e+01 2.660689e+01 2.024712e+01 2.069629e+01 1.994224e+01
CD99 1.021476e+02 1.249578e+02 1.252259e+02 2.395433e+02 8.420773e+01 2.802410e+02
HS3ST1 7.995198e+00 1.527261e+01 4.530883e+00 9.125460e+00 5.047875e+00 7.347142e+00
AOC1 1.909301e+00 0.000000e+00 8.676159e-01 0.000000e+00 5.506772e-01 1.574388e+00
WNT16 1.551307e+00 1.666103e+01 2.892053e-01 1.425853e+00 0.000000e+00 5.772754e+00
HECW1 5.966566e-01 1.388419e+00 1.253223e+00 2.566536e+00 9.177954e-02 1.364469e+01
MAD1L1 1.563240e+01 1.388419e+01 1.725592e+01 1.083648e+01 1.725455e+01 5.772754e+00
LASP1 2.081138e+02 1.332883e+02 2.322318e+02 2.871668e+02 2.666654e+02 1.810546e+02
SNX11 6.085897e+00 2.776839e+00 1.388185e+01 9.695802e+00 8.168379e+00 6.297550e+00
TMEM176A 6.085897e+00 8.330517e+00 2.265441e+01 3.963872e+01 4.405418e+00 3.253734e+01
M6PR 3.699271e+01 1.110736e+01 3.846430e+01 2.281365e+01 3.386665e+01 7.871938e+00
KLHL13 7.159879e-01 6.942097e+00 1.253223e+00 1.140683e+00 8.260158e-01 0.000000e+00
CYP26B1 1.157514e+01 4.859468e+01 1.513508e+01 8.897324e+01 7.067024e+00 7.294662e+01
X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet
TSPAN6 9.424599 1.207567e+01 4.740855e+01 8.079465e+00 3.757062e+00 3.001096e+01
DPM1 0.000000 1.380077e+01 4.740855e+00 1.253710e+01 1.202260e+01 1.385121e+01
SCYL3 1.346371 6.612869e+00 6.321140e+00 0.000000e+00 7.514123e-01 4.617070e+00
C1orf112 0.000000 1.150064e+00 0.000000e+00 8.358067e-01 0.000000e+00 1.154268e+00
FGR 86.167758 5.232792e+01 3.160570e+01 1.317789e+02 8.641242e+01 5.655911e+01
CFH 26.927424 2.875160e+00 1.580285e+01 1.114409e+00 1.051977e+01 8.079873e+00
FUCA2 10.770970 1.523835e+01 0.000000e+00 6.965056e+00 5.259886e+00 2.885669e+01
GCLC 30.966538 1.380077e+01 1.264228e+01 1.504452e+01 1.427683e+01 2.077682e+01
NFYA 30.966538 4.226486e+01 3.318599e+01 1.699474e+01 1.127118e+01 4.386217e+01
STPG1 5.385485 1.092561e+01 6.321140e+00 8.358067e+00 2.254237e+00 0.000000e+00
NIPAL3 29.620167 8.050449e+00 2.528456e+01 2.200958e+01 3.005649e+01 1.962255e+01
LAS1L 41.737508 2.788906e+01 4.108741e+01 4.262614e+01 2.479661e+01 2.193108e+01
ENPP4 0.000000 8.050449e+00 4.740855e+00 5.572045e-01 1.502825e+00 0.000000e+00
SEMA3F 28.273796 4.456498e+01 1.738314e+01 4.206894e+01 3.531638e+01 5.655911e+01
ANKIB1 18.849197 9.775545e+00 1.422257e+01 1.532312e+01 9.768360e+00 4.617070e+00
CYP51A1 39.044765 6.325353e+00 0.000000e+00 1.142269e+01 1.127118e+01 6.925605e+00
KRIT1 14.810083 8.625481e+00 0.000000e+00 1.086549e+01 7.514123e-01 1.154268e+01
RAD52 5.385485 9.775545e+00 0.000000e+00 6.129249e+00 2.254237e+00 0.000000e+00
MYH16 0.000000 0.000000e+00 6.321140e+00 0.000000e+00 0.000000e+00 0.000000e+00
BAD 78.089531 4.887773e+01 3.318599e+01 6.129249e+01 1.577966e+01 3.347376e+01
LAP3 9.424599 5.089034e+01 2.212399e+01 2.256678e+01 4.057627e+01 9.234140e+00
CD99 273.313358 1.581338e+02 2.101779e+02 1.755194e+02 2.088926e+02 1.927627e+02
HS3ST1 37.698394 1.638841e+01 3.476627e+01 1.588033e+01 2.705084e+01 1.154268e+00
AOC1 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 1.502825e+00 1.038841e+01
WNT16 0.000000 0.000000e+00 1.106200e+01 0.000000e+00 8.265536e+00 6.925605e+00
HECW1 0.000000 2.300128e+00 7.901426e+00 4.457636e+00 3.005649e+00 0.000000e+00
MAD1L1 0.000000 1.236319e+01 0.000000e+00 1.281570e+01 1.427683e+01 1.154268e+00
LASP1 192.531084 2.308754e+02 2.670682e+02 2.178670e+02 2.705084e+02 1.939169e+02
SNX11 2.692742 9.775545e+00 1.580285e+00 3.621829e+00 3.005649e+00 1.154268e+00
TMEM176A 9.424599 2.702651e+01 3.634656e+01 1.532312e+01 4.358192e+01 2.193108e+01
M6PR 13.463712 3.248931e+01 1.422257e+01 2.312399e+01 2.103955e+01 1.962255e+01
KLHL13 0.000000 2.012612e+00 0.000000e+00 5.572045e-01 0.000000e+00 0.000000e+00
CYP26B1 44.430250 3.565199e+01 3.634656e+01 2.841743e+01 6.236722e+01 2.654815e+01
X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet
TSPAN6 1.429542e+01 5.262119e+00 6.552841e+00 4.263451e+00 3.224208e+00 1.959330e+01
DPM1 1.965620e+01 1.195936e+01 9.707912e+00 1.899174e+01 9.770326e+00 8.163875e+00
SCYL3 8.934639e-01 2.072956e+00 3.640467e+00 5.426210e+00 3.908131e+00 9.796650e+00
C1orf112 8.934639e-01 4.783744e-01 2.426978e-01 4.263451e+00 5.862196e-01 0.000000e+00
FGR 7.505096e+01 5.923870e+01 3.470579e+01 3.410761e+01 4.396647e+01 8.408791e+01
CFH 8.934639e-01 3.109434e+00 2.912374e+00 6.976556e+00 5.178273e+00 8.163875e-01
FUCA2 8.934639e+00 1.642419e+01 2.888104e+01 1.472829e+01 9.868030e+00 2.938995e+01
GCLC 1.697581e+01 2.431737e+01 1.893043e+01 2.558071e+01 2.706380e+01 2.938995e+01
NFYA 1.786928e+01 2.814436e+01 3.179341e+01 3.216968e+01 2.559825e+01 2.204246e+01
STPG1 6.254247e+00 4.066182e+00 9.707912e-01 5.813797e+00 2.442582e+00 1.877691e+01
NIPAL3 4.467319e+00 1.259719e+01 8.494423e+00 4.651038e+00 1.074736e+01 1.551136e+01
LAS1L 5.182090e+01 3.428350e+01 2.475518e+01 2.519312e+01 3.488006e+01 3.837021e+01
ENPP4 8.934639e-01 4.863473e+00 4.125863e+00 1.240277e+01 1.856362e+00 0.000000e+00
SEMA3F 1.965620e+01 4.249559e+01 4.975305e+01 4.573520e+01 7.230041e+01 4.245215e+01
ANKIB1 8.934639e+00 1.714175e+01 1.067870e+01 1.511587e+01 1.172439e+01 1.796053e+01
CYP51A1 1.697581e+01 1.578636e+01 1.917313e+01 1.937932e+01 1.309224e+01 1.877691e+01
KRIT1 3.573855e+00 1.028505e+01 1.043601e+01 1.240277e+01 8.597887e+00 4.898325e+00
RAD52 1.965620e+01 1.012559e+01 1.310568e+01 8.914489e+00 8.793294e+00 1.061304e+01
MYH16 0.000000e+00 7.972907e-02 0.000000e+00 0.000000e+00 5.862196e-01 8.163875e-01
BAD 6.254247e+01 3.579835e+01 5.096654e+01 7.054074e+01 5.275976e+01 2.122608e+01
LAP3 5.450130e+01 4.839554e+01 3.033723e+01 3.139450e+01 4.416187e+01 1.877691e+01
CD99 2.876954e+02 2.217265e+02 4.303032e+02 1.996070e+02 2.208094e+02 1.200090e+02
HS3ST1 1.608235e+01 2.216468e+01 2.184280e+01 4.030899e+01 2.931098e+01 9.796650e+00
AOC1 7.147711e+00 1.195936e+00 9.707912e-01 3.488278e+00 0.000000e+00 0.000000e+00
WNT16 2.680392e+00 4.145912e+00 6.552841e+00 2.713105e+00 1.172439e+00 4.081938e+00
HECW1 5.360783e+00 1.355394e+00 7.280934e+00 9.689662e+00 1.563252e+00 3.265550e+00
MAD1L1 1.429542e+01 9.886404e+00 4.368561e+00 1.085242e+01 5.178273e+00 8.163875e-01
LASP1 1.974555e+02 2.816031e+02 3.152645e+02 2.166608e+02 2.610631e+02 2.024641e+02
SNX11 1.161503e+01 7.653991e+00 7.766330e+00 2.713105e+00 4.689757e+00 7.347488e+00
TMEM176A 6.611633e+01 2.367953e+01 1.286298e+01 5.387452e+01 8.568576e+01 3.592105e+01
M6PR 1.161503e+01 2.096875e+01 2.087201e+01 2.015450e+01 2.510974e+01 2.285885e+01
KLHL13 2.680392e+00 9.567488e-01 0.000000e+00 3.875865e-01 1.172439e+00 0.000000e+00
CYP26B1 2.233660e+01 3.547944e+01 5.266543e+01 3.449520e+01 4.719068e+01 3.673744e+01
X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6 1.582542e+01 1.497217e+00 1.320607e+01 5.926308e+00 9.711409e+00 7.254402e+00
DPM1 1.012827e+01 1.247681e+01 1.097120e+01 9.482092e+00 2.631479e+01 3.109029e+01
SCYL3 2.532068e+00 1.996290e+00 3.250725e+00 4.978098e+00 1.879628e+00 1.036343e+00
C1orf112 1.266034e+00 0.000000e+00 1.219022e+00 0.000000e+00 0.000000e+00 0.000000e+00
FGR 5.908158e+01 6.737479e+01 4.266576e+01 4.432878e+01 1.206094e+02 9.534356e+01
CFH 2.110056e-01 9.482377e+00 4.876087e+00 3.081680e+00 1.253085e+01 1.036343e+01
FUCA2 2.363263e+01 4.990725e+00 1.259656e+01 2.489049e+01 1.879628e+01 0.000000e+00
GCLC 1.772447e+01 7.985160e+00 1.665996e+01 1.849008e+01 1.315739e+01 1.450880e+01
NFYA 2.489866e+01 1.547125e+01 2.763116e+01 1.137851e+01 1.660338e+01 3.523566e+01
STPG1 7.596203e+00 2.994435e+00 5.079257e+00 8.296831e+00 0.000000e+00 9.327088e+00
NIPAL3 1.920151e+01 3.094249e+01 1.401875e+01 1.540840e+01 1.472375e+01 1.554515e+01
LAS1L 2.764174e+01 2.794806e+01 4.002455e+01 3.413553e+01 3.665274e+01 2.072686e+01
ENPP4 5.064135e+00 5.489797e+00 1.828533e+00 2.133471e+00 3.445984e+00 2.072686e+00
SEMA3F 4.030208e+01 2.994435e+01 4.043089e+01 4.006184e+01 3.915891e+01 2.383589e+01
ANKIB1 1.477039e+01 1.048052e+01 1.279973e+01 8.533883e+00 8.145053e+00 6.218058e+00
CYP51A1 1.624743e+01 1.347496e+01 1.097120e+01 2.441639e+01 2.130245e+01 1.865418e+01
KRIT1 1.308235e+01 5.988870e+00 8.939492e+00 1.232672e+01 1.566356e+00 2.176320e+01
RAD52 1.244933e+01 8.484232e+00 3.657065e+00 4.978098e+00 4.385798e+00 4.145372e+00
MYH16 0.000000e+00 4.491652e+00 4.063406e-01 0.000000e+00 0.000000e+00 4.145372e+00
BAD 3.903604e+01 5.988870e+01 4.185308e+01 5.689255e+01 5.325612e+01 2.487223e+01
LAP3 2.468766e+01 4.192209e+01 4.896404e+01 4.290647e+01 2.067590e+01 4.456275e+01
CD99 2.572159e+02 3.378721e+02 1.800089e+02 2.652615e+02 1.873362e+02 1.544151e+02
HS3ST1 1.688045e+01 1.147867e+01 1.422192e+01 4.006184e+01 7.831782e+00 1.865418e+01
AOC1 0.000000e+00 4.990725e-01 1.219022e+00 0.000000e+00 0.000000e+00 0.000000e+00
WNT16 1.202732e+01 3.144157e+01 3.271042e+01 5.025509e+01 1.378394e+01 3.109029e+01
HECW1 5.486146e+00 1.497217e+00 1.015851e+00 7.348622e+00 3.759255e+00 6.218058e+00
MAD1L1 4.642124e+00 7.486087e+00 2.031703e+00 1.019325e+01 1.566356e+01 1.554515e+01
LASP1 2.489866e+02 2.764862e+02 2.027639e+02 2.363411e+02 1.835770e+02 1.792874e+02
SNX11 8.018214e+00 8.484232e+00 7.517300e+00 4.266942e+00 6.891968e+00 0.000000e+00
TMEM176A 4.093509e+01 3.493507e+01 1.848850e+01 2.157176e+01 1.910955e+01 1.865418e+01
M6PR 2.574269e+01 2.495362e+01 2.377092e+01 2.868333e+01 1.722992e+01 3.109029e+01
KLHL13 4.009107e+00 4.990725e-01 1.422192e+00 3.555785e+00 0.000000e+00 0.000000e+00
CYP26B1 9.347550e+01 6.837293e+01 6.074791e+01 9.885081e+01 5.826846e+01 5.803521e+01
[ reached getOption("max.print") -- omitted 23994 rows ]
$tibia_pellet_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) batchX104 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99 groupTSP
TSPAN6 -12.610185 0.4656040 0.4422852 0.403703919 0.1754379 0.07721806 -1.42111406 0.8163995 1.9487877 0.5237170 1.7986388 0.4312905 -0.01883094 1.54257119 -0.7846454 0.9754909 0.8447905 0.2784391
DPM1 -11.083391 0.1452394 -0.5819926 -0.003630514 0.4987407 0.19237705 0.06287435 -0.8849777 -0.3611997 -0.1129534 0.2262298 -0.2406732 0.01120677 -0.36878805 -0.2061841 -0.2949793 0.7434959 -0.2240774
SCYL3 -12.426941 -0.5980406 0.4075137 -0.378306360 0.2538103 0.10490639 -0.84409581 -0.8038386 0.4695531 -2.6876004 -0.4053860 -0.3610354 0.13565891 0.38868046 -0.6844480 0.0103843 -0.9504596 0.0350321
C1orf112 -12.628526 -0.1477432 -3.1477035 -1.868910431 -0.4231967 0.39337781 0.05645284 -4.5658604 -1.1691027 -1.5266838 -0.2378015 -1.3703593 0.15351523 0.04966391 -4.8451503 -1.3593868 -4.6089035 -1.6974468
FGR -7.253647 -1.7912528 -1.7319488 -1.544142527 -0.9514118 -1.20217369 -0.14271566 -1.6133817 -2.5670434 -1.5967492 -2.0056865 -2.4538622 -2.52084164 -2.00425301 -2.3512102 -2.4509715 -1.5838103 -0.5866547
24022 more rows ...
$fitted.values
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6 41.85611 13.702649 17 3.30000e+01 53.210277 11.5505717 33.02783
DPM1 194.20455 38.349663 57 3.30000e+01 163.568295 21.4172458 211.85433
SCYL3 50.38540 12.931923 7 3.00000e+01 29.074051 4.9479608 42.99219
C1orf112 41.13761 1.651918 9 7.83076e-08 5.037821 0.1341388 17.90267
FGR 8957.13096 1231.443111 379 3.36000e+02 1616.265906 147.3399717 2289.77407
X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6 3.7590332 37.10990 16.612402 17 1.433036e+01 7.396822e+00 81.278981
DPM1 14.5442075 192.95117 52.101060 356 1.203640e+01 3.747495e+00 37.153314
SCYL3 3.8361761 45.85939 16.094728 37 3.369226e+00 1.363424e+00 22.189098
C1orf112 0.2499296 53.21360 2.921926 75 5.729235e-08 3.627342e-09 3.450147
FGR 109.4431596 2205.65288 414.647998 13368 2.685515e+02 5.821239e+01 188.804816
X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6 19.5824623 20.1331437 9.8850829 17.437944 29.8323314 64.08281 27.8775615
DPM1 5.3993707 49.1723863 14.5628556 16.672386 17.2046642 151.17964 39.6700835
SCYL3 4.1912293 0.8735848 0.3362688 2.291652 3.0736429 34.67399 11.8257820
C1orf112 0.1019602 2.4367929 0.1467544 2.329870 0.4889085 10.12901 0.5404858
FGR 19.1030155 514.3496706 106.0539866 82.468882 59.2491107 762.49670 139.2999750
X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6 8.383436 44.039664 19.073853 97.724435 3.000000e+00 43.437426 49.2994999
DPM1 40.025150 126.826928 12.985872 40.132146 2.500000e+01 56.183724 38.4632066
SCYL3 11.768332 48.467387 7.207121 28.949380 4.000000e+00 19.785543 17.6051263
C1orf112 10.169781 6.552959 4.602971 2.892723 3.250778e-08 3.924222 0.5463059
FGR 146.686261 323.602013 116.765917 251.235289 1.350000e+02 300.093927 143.0327358
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6 2.470622e+01 9.889762e+00
DPM1 1.031048e+02 2.489515e+01
SCYL3 4.864856e+00 1.526730e+00
C1orf112 9.579693e-08 4.703649e-09
FGR 4.633886e+02 7.789769e+01
24022 more rows ...
$deviance
[1] 24.200853 8.965046 6.471256 8.067473 19.107276
24022 more elements ...
$iter
[1] 11 6 9 18 10
24022 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
24022 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_pellet X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_pellet X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_pellet
TSPAN6 3 28 17 33 75 6 4
DPM1 177 42 57 33 153 23 159
SCYL3 61 10 7 30 24 6 16
C1orf112 71 0 9 0 6 0 23
FGR 13362 623 379 336 1662 143 3327
X130_Tibia_sclerotic_pellet X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_pellet X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_pellet
TSPAN6 9 26 22 17 15 7 42
DPM1 19 218 45 356 20 0 48
SCYL3 7 38 19 37 4 1 23
C1orf112 0 37 4 75 0 0 4
FGR 57 3506 167 13368 244 64 182
X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_pellet
TSPAN6 30 29 5 26 16 66 27
DPM1 3 45 16 12 22 150 40
SCYL3 4 0 1 4 1 26 15
C1orf112 0 3 0 1 1 6 1
FGR 20 473 115 49 84 743 143
X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_pellet X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet
TSPAN6 11 33 24 75 3 65 25
DPM1 49 100 10 48 25 54 40
SCYL3 14 40 12 12 4 16 21
C1orf112 11 6 0 6 0 6 0
FGR 88 450 103 280 135 210 187
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6 31 7
DPM1 84 30
SCYL3 6 1
C1orf112 0 0
FGR 385 92
24022 more rows ...
$unshrunk.coefficients
(Intercept) batchX104 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99 groupTSP
TSPAN6 -12.619632 0.4701909 0.4455788 0.408045364 0.1756204 0.07877449 -1.44417833 0.8217560 1.9555322 0.5285186 1.8062359 0.4351765 -0.01743710 1.5495737 -0.7922702 0.981732013 0.8504908 0.28082888
DPM1 -11.084958 0.1453547 -0.5835778 -0.003649709 0.4994948 0.19265367 0.06286493 -0.8873633 -0.3619764 -0.1131907 0.2266670 -0.2412049 0.01113898 -0.3695569 -0.2066808 -0.295636426 0.7445070 -0.22468863
SCYL3 -12.434168 -0.6025760 0.4081589 -0.381823806 0.2538249 0.10500699 -0.85193744 -0.8114053 0.4717821 -2.7944625 -0.4086031 -0.3644733 0.13625359 0.3908611 -0.6900518 0.009898445 -0.9599909 0.03747496
C1orf112 -12.636947 -0.1484828 -17.2978979 -1.931917556 -0.4194654 0.45651978 0.05741150 -18.4984082 -1.1866233 -1.5658509 -0.1892849 -1.3922806 0.19304086 0.1452724 -19.1153538 -1.405106264 -18.5002846 -1.81750801
FGR -7.253665 -1.7914536 -1.7321705 -1.544299809 -0.9514890 -1.20229793 -0.14273999 -1.6135492 -2.5676089 -1.5969128 -2.0059590 -2.4543688 -2.52136627 -2.0045409 -2.3515751 -2.451461283 -1.5839658 -0.58678562
24022 more rows ...
$df.residual
[1] 12 12 12 12 12
24022 more elements ...
$design
(Intercept) batchX104 batchX109 batchX128 batchX130 batchX144 batchX148 batchX149 batchX151 batchX155 batchX156 batchX159 batchX160 batchX161 batchX163 batchX164 batchX99 groupTSP
X102_tibia_non.sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X102_tibia_sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
X104_tibia_non.sclerotic_pellet 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X109_tibia_sclerotic_pellet 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
X128_tibia_non.sclerotic_pellet 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
25 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 16.35387 14.95639 14.98265 15.38973 16.18584 14.37749 15.94136 13.48734 16.15474 15.07018 16.89702 14.46026 13.5181 15.06199 13.35791 15.09348 14.10131 13.67204 13.92816 16.34463 15.23145 14.76333 16.14133 14.01838
[,25] [,26] [,27] [,28] [,29] [,30]
[1,] 15.37138 14.51051 15.40922 15.25499 14.9762 13.77981
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 30
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
24022 more rows ...
$dispersion
[1] 0.3716027 0.2763020 0.7333519 1.5146132 0.1501162
24022 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 3.2027643 3.8533938 1.9688435 0.7447871 7.2331615
24022 more elements ...
$df.residual.zeros
[1] 12 12 12 10 12
24022 more elements ...
$df.prior
[1] 50.465175 56.309244 56.309244 56.309244 9.321503
24022 more elements ...
$var.post
[1] 1.366888 1.018743 1.224142 1.276124 1.156304
24022 more elements ...
$var.prior
[1] 1.212362 1.076636 1.370094 1.359481 0.595060
24022 more elements ...
$samples25 more rows ...
$genes24022 more rows ...
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 0.8260483
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.9351571
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 0.8723237
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 3.548994
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$text
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 1.179955 1.179955
$tibia_pellet_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 3.237275 2.925556
$tibia_pellet_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$tibia_pellet_sclerotic_vs_non_sclerotic$boxplot_gg
$tibia_sclerotic_vs_non_sclerotic
$tibia_sclerotic_vs_non_sclerotic$name
[1] "sclerotic-vs-non.sclerotic"
$tibia_sclerotic_vs_non_sclerotic$results
Coefficient: groupsclerotic
$tibia_sclerotic_vs_non_sclerotic$colsums_samples
$tibia_sclerotic_vs_non_sclerotic$normalized_matrix
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6 2.665806e-01 5.996075e+00 9.124057e+00 4.544512e+00 5.377963e+00 1.807617e+01
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 3.163508e-01 6.952371e+00
DPM1 1.572826e+01 9.660343e+00 1.368609e+01 1.249741e+01 1.803199e+01 4.171423e+00
SCYL3 5.420472e+00 8.660997e+00 3.258592e+00 9.846443e+00 2.214455e+00 9.733320e+00
C1orf112 6.309074e+00 0.000000e+00 0.000000e+00 0.000000e+00 2.847157e+00 0.000000e+00
FGR 1.187350e+03 3.864137e+01 2.030103e+02 1.378502e+02 1.198969e+02 2.224759e+01
CFH 7.997418e-01 1.332461e+00 3.584451e+00 4.165803e+00 1.581754e+00 1.390474e+00
FUCA2 1.226271e+01 2.598299e+01 1.889983e+01 1.249741e+01 6.010665e+00 4.171423e+00
GCLC 5.136120e+01 2.531676e+01 1.955155e+01 2.764578e+01 1.676659e+01 5.909516e+01
NFYA 6.051380e+01 1.732199e+01 3.486693e+01 5.339802e+01 3.922750e+01 3.337138e+01
STPG1 2.310365e+00 1.065969e+01 6.191325e+00 3.787093e-01 3.479859e+00 6.952371e-01
NIPAL3 1.866064e+01 8.660997e+00 1.042749e+01 4.165803e+00 5.061612e+00 1.599045e+01
LAS1L 5.287182e+01 3.031349e+01 3.747381e+01 8.748186e+01 7.307703e+01 3.406662e+01
ENPP4 1.377333e+01 0.000000e+00 4.562029e+00 2.272256e+00 3.163508e+00 6.952371e-01
SEMA3F 1.510623e+00 3.997383e+01 2.248428e+01 8.748186e+01 7.624054e+01 4.797136e+01
ANKIB1 8.086278e+00 1.332461e+01 1.368609e+01 1.211870e+01 1.265403e+01 1.251427e+01
X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6 4.489760e+00 9.815976e+00 1.012778e+01 6.987206e+00 7.073169e+00 7.104785e+00
TNMD 1.496587e+00 9.131141e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.478382e+00 1.597950e+01 1.395383e+01 6.987206e+00 1.503049e+01 1.449376e+01
SCYL3 2.993173e+00 2.282785e+00 2.925804e+00 6.352005e+00 1.768292e+00 2.273531e+00
C1orf112 0.000000e+00 2.282785e-01 4.951360e+00 0.000000e+00 0.000000e+00 5.683828e-01
FGR 6.535095e+01 3.903563e+01 8.214757e+01 7.114246e+01 3.713414e+01 1.574420e+02
CFH 6.485209e+00 4.109013e+00 5.176422e+00 2.540802e+00 1.768292e+00 6.631133e-01
FUCA2 1.297042e+01 1.164220e+01 1.755482e+01 1.757388e+01 1.989329e+01 1.070454e+01
GCLC 8.979520e+00 3.287211e+01 3.533471e+01 1.058668e+01 2.652439e+01 2.728238e+01
NFYA 5.238053e+01 2.008851e+01 1.823001e+01 3.218349e+01 1.635670e+01 3.306093e+01
STPG1 5.487485e+00 2.739342e+00 6.301732e+00 8.469340e-01 1.768292e+00 4.925985e+00
NIPAL3 1.297042e+01 3.195899e+00 8.102226e+00 1.249228e+01 1.237805e+01 1.676729e+01
LAS1L 4.140557e+01 4.634054e+01 4.838830e+01 2.265549e+01 3.492377e+01 4.897565e+01
ENPP4 4.988622e-01 6.163520e+00 1.800495e+00 3.387736e+00 2.210365e+00 8.052090e+00
SEMA3F 3.292491e+01 1.506638e+01 2.543199e+01 5.293338e+01 1.989329e+01 5.797505e+01
ANKIB1 1.446700e+01 1.369671e+01 9.902721e+00 1.079841e+01 1.414634e+01 1.676729e+01
X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6 4.639109e+00 3.425506e+00 7.789427e+00 5.098613e-01 2.965000e+00 1.277946e+01
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 5.566931e+00 1.313111e+01 1.057137e+01 2.026699e+01 1.284833e+01 2.697887e+01
SCYL3 4.639109e+00 3.425506e+00 2.225551e+00 2.039445e+00 0.000000e+00 9.939583e+00
C1orf112 0.000000e+00 0.000000e+00 5.563876e-01 2.931702e+00 0.000000e+00 0.000000e+00
FGR 3.247377e+01 8.164123e+01 2.250588e+02 4.240771e+02 1.976667e+02 8.093660e+01
CFH 0.000000e+00 3.996424e+00 1.112775e+00 7.647919e-01 3.953334e+00 5.679762e+00
FUCA2 1.577297e+01 1.998212e+01 1.112775e+01 1.249160e+01 1.186000e+01 2.839881e+00
GCLC 3.618505e+01 5.138259e+00 3.727797e+01 6.436999e+01 2.569667e+01 2.697887e+01
NFYA 5.381367e+01 3.825148e+01 2.726299e+01 3.887692e+01 1.680167e+01 2.555893e+01
STPG1 2.783466e+00 1.541478e+01 6.954846e+00 3.951425e+00 0.000000e+00 1.277946e+01
NIPAL3 8.350397e+00 2.797497e+01 1.780440e+01 1.835501e+01 3.953334e+00 1.703928e+01
LAS1L 3.247377e+01 2.283671e+01 2.921035e+01 4.078890e+01 1.087167e+01 3.691845e+01
ENPP4 3.711287e+00 3.425506e+00 1.446608e+01 6.118336e+00 3.953334e+00 4.259821e+00
SEMA3F 2.041208e+01 3.140047e+01 4.200727e+01 3.046421e+01 1.482500e+01 1.845923e+01
ANKIB1 3.154594e+01 9.705600e+00 1.224053e+01 1.057962e+01 1.581334e+01 1.135952e+01
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6 4.663119e+00 2.638924e+00 7.302665e+00 6.425066e+00 5.400705e+00 8.535784e-01
TNMD 7.174029e-02 0.000000e+00 0.000000e+00 2.044339e+00 4.909732e-01 0.000000e+00
DPM1 1.248281e+01 2.212637e+01 1.236742e+01 1.314218e+01 1.652943e+01 1.787494e+01
SCYL3 3.587015e+00 3.856889e+00 3.651333e+00 5.548920e+00 2.945839e+00 1.857788e+00
C1orf112 1.147845e+00 3.755392e+00 1.648989e+00 1.168194e+00 3.109497e+00 3.765787e+00
FGR 2.292102e+02 3.558488e+02 1.110712e+02 4.877209e+01 2.459776e+02 6.712139e+02
CFH 1.793507e+00 4.059884e-01 2.591268e+00 4.672775e+00 3.273155e-01 3.012630e-01
FUCA2 1.535242e+01 1.867546e+01 1.613653e+01 4.964824e+00 1.587480e+01 1.004210e+01
GCLC 4.655945e+01 4.932759e+01 3.015294e+01 7.301211e+00 7.282769e+01 1.056931e+02
NFYA 3.099181e+01 3.867039e+01 2.697275e+01 2.686846e+01 4.271467e+01 5.392607e+01
STPG1 7.460991e+00 4.567369e+00 1.884559e+00 1.752291e+00 9.001175e+00 4.920628e+00
NIPAL3 1.528068e+01 1.847247e+01 6.595956e+00 2.131954e+01 1.472920e+01 1.978293e+01
LAS1L 3.594189e+01 4.821112e+01 3.474655e+01 4.088678e+01 3.665933e+01 6.095554e+01
ENPP4 2.726131e+00 8.018270e+00 3.415763e+00 3.504581e+00 4.582417e+00 3.163261e+00
SEMA3F 2.518084e+01 9.540726e+00 1.448755e+01 3.562991e+01 4.778806e+01 1.044378e+01
ANKIB1 1.205237e+01 7.307790e+00 1.531204e+01 2.394797e+01 1.652943e+01 8.636205e+00
X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6 1.016659e+01 1.255970e+01 7.875201e+00 11.202808 9.341971 1.786584e+00
TNMD 0.000000e+00 2.767391e+00 0.000000e+00 0.000000 0.000000 0.000000e+00
DPM1 2.323792e+01 1.404983e+01 1.050027e+01 9.165934 0.000000 1.161279e+01
SCYL3 2.904739e+00 2.554515e+00 2.100054e+00 7.129059 1.334567 4.913105e+00
C1orf112 0.000000e+00 0.000000e+00 0.000000e+00 0.678958 0.000000 0.000000e+00
FGR 4.560441e+02 5.194180e+01 1.281033e+02 51.940290 85.412310 3.215850e+01
CFH 0.000000e+00 5.534782e+00 7.350188e+00 4.413227 26.691347 5.359751e+00
FUCA2 4.357109e+00 1.681722e+01 6.300161e+00 15.616035 10.676539 2.813869e+01
GCLC 1.219991e+02 3.406020e+01 1.470038e+01 16.634472 30.695049 2.813869e+01
NFYA 5.809479e+01 3.086705e+01 5.775147e+00 35.984776 30.695049 1.473931e+01
STPG1 8.714218e+00 5.109029e+00 2.100054e+00 7.808018 5.338269 1.205944e+01
NIPAL3 5.809479e+00 8.727925e+00 8.400214e+00 12.221245 29.360482 4.913105e+00
LAS1L 2.178555e+01 3.427307e+01 3.097579e+01 26.479364 41.371588 3.573167e+01
ENPP4 4.357109e+00 1.213394e+01 2.100054e+00 4.752706 0.000000 1.607925e+01
SEMA3F 1.742844e+01 2.703528e+01 3.097579e+01 33.268944 28.025914 1.831248e+01
ANKIB1 0.000000e+00 1.341120e+01 6.300161e+00 13.918640 18.683943 2.054571e+01
X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6 1.194617e+01 0.000000e+00 4.642600e+01 5.081543e+00 8.020405e+00 7.182311e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.365277e+01 2.613187e+01 4.642600e+00 1.134484e+01 1.244546e+01 1.256904e+01
SCYL3 6.541952e+00 0.000000e+00 6.190134e+00 2.481684e+00 0.000000e+00 4.488945e-01
C1orf112 1.137731e+00 0.000000e+00 0.000000e+00 3.545262e-01 8.296971e-01 0.000000e+00
FGR 5.176675e+01 1.498227e+02 3.095067e+01 5.566062e+01 1.308156e+02 5.207176e+01
CFH 2.844327e+00 8.710623e+00 1.547533e+01 2.127157e+00 1.106263e+00 5.835628e+00
FUCA2 1.507493e+01 1.393700e+01 0.000000e+00 1.359017e+01 6.914143e+00 2.558698e+01
GCLC 1.365277e+01 2.264762e+01 1.238027e+01 3.592533e+01 1.493455e+01 9.426783e+00
NFYA 4.181161e+01 0.000000e+00 3.249820e+01 2.221698e+01 1.687051e+01 2.828035e+01
STPG1 1.080844e+01 0.000000e+00 6.190134e+00 5.672420e+00 8.296971e+00 2.693367e+00
NIPAL3 7.964115e+00 1.742125e+01 2.476053e+01 1.146302e+01 2.184869e+01 7.182311e+00
LAS1L 2.758997e+01 1.742125e+01 4.023587e+01 4.396125e+01 4.231455e+01 4.533834e+01
ENPP4 7.964115e+00 0.000000e+00 4.642600e+00 6.854174e+00 5.531314e-01 6.284522e+00
SEMA3F 4.408707e+01 2.438974e+01 1.702287e+01 1.559915e+01 4.176142e+01 1.391573e+01
ANKIB1 9.670711e+00 1.393700e+01 1.392780e+01 1.902624e+01 1.521111e+01 7.631206e+00
X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6 3.695893e+00 9.342745e+00 2.915851e+01 2.459210e+00 1.434330e+01 9.752715e+00
TNMD 0.000000e+00 1.494839e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.182147e+00
DPM1 1.182686e+01 7.349626e+00 1.345777e+01 9.134209e+00 1.972204e+01 1.167370e+01
SCYL3 7.391787e-01 4.733657e+00 4.485924e+00 1.756579e+00 8.964565e-01 5.319663e+00
C1orf112 0.000000e+00 1.245699e+00 1.121481e+00 0.000000e+00 8.964565e-01 2.955368e-01
FGR 8.500555e+01 3.662356e+01 5.495257e+01 2.564605e+01 7.530235e+01 1.920989e+01
CFH 1.034850e+01 4.982797e-01 7.850367e+00 1.053947e+00 8.964565e-01 2.068758e+00
FUCA2 5.174251e+00 1.731522e+01 2.803703e+01 7.377630e+00 8.964565e+00 1.669783e+01
GCLC 1.404439e+01 3.151619e+01 2.018666e+01 2.599736e+01 1.703267e+01 3.310013e+01
NFYA 1.108768e+01 4.559260e+01 4.261628e+01 2.494342e+01 1.792913e+01 2.763269e+01
STPG1 2.217536e+00 9.342745e+00 0.000000e+00 1.405263e+00 6.275196e+00 3.694210e+00
NIPAL3 2.956715e+01 2.354372e+01 1.906518e+01 8.431577e+00 4.482283e+00 8.570568e+00
LAS1L 2.439290e+01 3.699727e+01 2.130814e+01 4.953552e+01 5.199448e+01 3.915863e+01
ENPP4 1.478357e+00 7.474196e+00 0.000000e+00 3.513157e+00 8.964565e-01 6.649579e+00
SEMA3F 3.474140e+01 3.276189e+01 5.495257e+01 3.161842e+01 1.972204e+01 2.659831e+01
ANKIB1 9.609323e+00 2.429114e+01 4.485924e+00 1.510658e+01 8.964565e+00 2.541617e+01
X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6 5.266122e+00 8.784613e+00 6.669063e+00 1.124806e+01 4.196805e+00 8.759837e+00
TNMD 3.989486e-01 1.421040e+00 0.000000e+00 9.998279e-01 0.000000e+00 3.322697e+00
DPM1 1.196846e+01 1.098077e+01 9.880093e+00 1.291444e+01 1.869486e+01 1.258597e+01
SCYL3 2.074533e+00 3.875565e-01 3.705035e+00 2.249613e+00 5.341389e+00 3.322697e+00
C1orf112 4.787383e-01 2.583710e-01 2.470023e-01 6.665519e-01 4.196805e+00 8.055022e-01
FGR 5.928376e+01 2.829162e+01 3.532133e+01 1.399759e+01 3.357444e+01 2.094306e+01
CFH 3.111799e+00 2.066968e+00 2.964028e+00 2.166294e+00 6.867500e+00 3.826136e+00
FUCA2 1.643668e+01 1.886108e+01 2.939328e+01 1.624720e+01 1.449805e+01 1.550592e+01
GCLC 2.433587e+01 4.211447e+01 1.926618e+01 3.699363e+01 2.518083e+01 3.373041e+01
NFYA 2.816577e+01 3.113370e+01 3.235730e+01 3.241109e+01 3.166680e+01 3.473728e+01
STPG1 4.069276e+00 5.813347e+00 9.880093e-01 8.165261e+00 5.722916e+00 8.256398e+00
NIPAL3 1.260678e+01 1.072240e+01 8.645081e+00 9.665003e+00 4.578333e+00 1.037084e+01
LAS1L 3.430958e+01 4.095180e+01 2.519424e+01 3.649372e+01 2.479930e+01 4.218818e+01
ENPP4 4.867173e+00 4.004750e+00 4.199040e+00 5.998967e+00 1.220889e+01 3.020633e+00
SEMA3F 4.252792e+01 1.847352e+01 5.063548e+01 2.082975e+01 4.502028e+01 2.728639e+01
ANKIB1 1.715479e+01 1.731086e+01 1.086810e+01 2.557893e+01 1.487958e+01 1.611004e+01
X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6 3.298954e+00 7.738225e+00 1.891786e+01 6.898157e+00 1.616451e+01 9.547951e+00
TNMD 0.000000e+00 9.401581e-01 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 9.996831e+00 1.923708e+01 7.882441e+00 8.779472e+00 1.034529e+01 1.291782e+01
SCYL3 3.998732e+00 3.182074e+00 9.458929e+00 2.383000e+00 2.586322e+00 1.067124e+01
C1orf112 5.998099e-01 6.508787e-01 0.000000e+00 1.128789e+00 1.293161e+00 0.000000e+00
FGR 4.498574e+01 4.223480e+01 8.118914e+01 4.496344e+01 6.034751e+01 2.527399e+01
CFH 5.298320e+00 2.169596e+00 7.882441e-01 1.630473e+00 2.155268e-01 1.123288e+00
FUCA2 1.009680e+01 1.113726e+01 2.837679e+01 1.141331e+01 2.413900e+01 1.572604e+01
GCLC 2.769122e+01 2.596283e+01 2.837679e+01 2.752992e+01 1.810425e+01 2.190412e+01
NFYA 2.619170e+01 4.049912e+01 2.128259e+01 2.959936e+01 2.543217e+01 1.291782e+01
STPG1 2.499208e+00 4.700791e+00 1.812961e+01 4.389736e+00 7.758966e+00 7.301375e+00
NIPAL3 1.099651e+01 1.193278e+01 1.497664e+01 1.329463e+01 1.961294e+01 5.616442e+00
LAS1L 3.568869e+01 3.876344e+01 3.704747e+01 2.677739e+01 2.823401e+01 2.639728e+01
ENPP4 1.899398e+00 5.207030e+00 0.000000e+00 4.264315e+00 5.172644e+00 3.369865e+00
SEMA3F 7.397655e+01 3.362873e+01 4.098869e+01 3.373826e+01 4.116562e+01 1.123288e+01
ANKIB1 1.199620e+01 1.815228e+01 1.734137e+01 1.617931e+01 1.508688e+01 5.054798e+00
X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6 1.482772e+00 1.965155e+00 2.321636e+01 1.333434e+01 5.937025e+00 1.341001e+00
TNMD 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
DPM1 1.235643e+01 3.275259e+00 1.428699e+01 1.107776e+01 9.499241e+00 8.381254e+00
SCYL3 1.977029e+00 3.930311e+00 4.911153e+00 3.282300e+00 4.987101e+00 0.000000e+00
C1orf112 0.000000e+00 0.000000e+00 4.464684e-01 1.230863e+00 0.000000e+00 0.000000e+00
FGR 6.672474e+01 1.319929e+02 2.366283e+01 4.308019e+01 4.440895e+01 9.923404e+01
CFH 9.390890e+00 1.310104e+00 4.464684e+00 4.923450e+00 3.087253e+00 2.346751e+00
FUCA2 4.942573e+00 3.308012e+01 1.294758e+01 1.271891e+01 2.493551e+01 1.139850e+01
GCLC 7.908118e+00 2.030661e+01 1.473346e+01 1.682179e+01 1.852352e+01 3.117826e+01
NFYA 1.532198e+01 1.473867e+01 2.053755e+01 2.789955e+01 1.139909e+01 3.453076e+01
STPG1 2.965544e+00 6.550518e+00 9.375837e+00 5.128594e+00 8.311836e+00 6.705003e-01
NIPAL3 3.064396e+01 1.506619e+01 1.651933e+01 1.415492e+01 1.543627e+01 1.575676e+01
LAS1L 2.767841e+01 4.323342e+01 3.125279e+01 4.041332e+01 3.419727e+01 4.559402e+01
ENPP4 5.436831e+00 2.620207e+00 2.232342e+00 1.846294e+00 2.137329e+00 7.710753e+00
SEMA3F 2.965544e+01 2.652960e+01 2.678811e+00 4.082361e+01 4.013429e+01 2.045026e+01
ANKIB1 1.037940e+01 1.604877e+01 2.768104e+01 1.292406e+01 8.549317e+00 1.676251e+01
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6 9.873680e+00 7.170684e+00
TNMD 0.000000e+00 0.000000e+00
DPM1 2.675449e+01 3.073150e+01
SCYL3 1.911035e+00 1.024383e+00
C1orf112 0.000000e+00 0.000000e+00
FGR 1.226247e+02 9.424327e+01
CFH 1.274023e+01 1.024383e+01
FUCA2 1.911035e+01 0.000000e+00
GCLC 1.337724e+01 1.434137e+01
NFYA 1.688081e+01 3.482903e+01
STPG1 0.000000e+00 9.219450e+00
NIPAL3 1.496977e+01 1.536575e+01
LAS1L 3.726518e+01 2.048767e+01
ENPP4 3.503564e+00 2.048767e+00
SEMA3F 3.981322e+01 2.356082e+01
ANKIB1 8.281151e+00 6.146300e+00
[ reached getOption("max.print") -- omitted 25439 rows ]
$tibia_sclerotic_vs_non_sclerotic$fit
An object of class "DGEGLM"
$coefficients
(Intercept) patientX104 patientX105 patientX109 patientX128 patientX130 patientX144 patientX148 patientX149 patientX151 patientX155 patientX156 patientX159 patientX160 patientX161 patientX163 patientX164
TSPAN6 -12.25172 0.04406928 0.84019247 0.60588199 0.16165295 0.1244473 0.06794798 -0.02625455 0.7528399 1.07888329 0.22129102 1.01215762 0.4478837 0.358302596 0.9182398 -0.12645603 1.0748605
TNMD -17.07707 1.59157950 4.95629013 2.32100432 -0.21219890 -0.2794509 3.49152043 1.82692534 3.1336725 -0.26591528 -0.18256384 2.66132364 3.5603833 4.140584975 2.1456256 -0.07524611 -0.1091402
DPM1 -11.15592 0.06873637 -0.62448403 -0.06318352 -0.09346094 0.2743371 0.11620614 0.33543622 -0.4111354 0.03501757 -0.09771562 -0.08282952 -0.1776007 0.006748076 -0.1329719 -0.39529075 -0.1662029
SCYL3 -11.98020 -0.03834093 0.04117712 -0.38786677 -0.68384443 -0.5999563 -0.34575741 -0.87746903 -0.5255504 -0.25832922 -1.75449122 -0.68998705 -0.7370011 -0.463595136 -0.3606641 -0.09923204 -0.3076573
C1orf112 -12.94608 -0.48959117 -4.04063893 0.71374233 -2.08926183 -0.6449300 0.32655119 0.12371514 -1.5649092 -1.52956438 -1.68616890 -0.69943085 -1.4028547 -0.052684280 -0.1845621 -4.17846401 -1.2934729
patientX99 groupsclerotic
TSPAN6 0.2287480 0.04349959
TNMD -0.2980981 -0.93351400
DPM1 0.4825022 -0.14390015
SCYL3 -1.8057150 -0.11344632
C1orf112 -4.4298734 -1.06861775
25450 more rows ...
$fitted.values
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6 5.344491e+01 1.489758e+01 1.522931e+01 13.1146519 15.6997911 1.588054e+01
TNMD 2.409608e-09 1.508575e-10 1.542168e-10 0.4309118 0.5158525 9.596770e+00
DPM1 1.605415e+02 3.707124e+01 3.789672e+01 40.3520364 48.3061652 1.097138e+01
SCYL3 7.028191e+01 1.671522e+01 1.708743e+01 15.8584516 18.9844442 9.357692e+00
C1orf112 2.649991e+01 2.212895e+00 2.262171e+00 3.7937869 4.5416121 3.201364e-08
X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6 2.312673e+01 38.234234 40.5239878 43.0749164 1.264395e+01 5.900477e+01
TNMD 3.138956e+00 1.655666 0.3941339 0.4189441 3.773348e-10 1.760886e-09
DPM1 1.323581e+01 58.658034 51.5024375 54.7444442 2.938504e+01 1.371294e+02
SCYL3 1.162725e+01 18.526529 16.7537931 17.8084210 7.097339e+00 3.312073e+01
C1orf112 1.396661e-08 23.082183 7.3289843 7.7903337 6.070175e-01 2.832733e+00
X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6 6.295189e+00 1.023057e+01 1.934575e+01 4.222221e+01 5.690182e+00 3.960587e+00
TNMD 4.219531e-11 6.857334e-11 5.598321e-10 1.221837e-09 3.698364e-11 2.574204e-11
DPM1 1.211973e+01 1.969627e+01 6.749719e+01 1.473130e+02 1.644624e+01 1.144722e+01
SCYL3 3.014956e+00 4.899729e+00 1.226809e+01 2.677517e+01 3.078766e+00 2.142940e+00
C1orf112 9.053873e-02 1.471382e-01 4.435651e+00 9.680835e+00 3.908455e-01 2.720436e-01
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6 70.89719 50.11163 45.123111 18.198427 28.253889 92.09166
TNMD 27.96827 19.76857 3.998038 1.612433 1.321478 4.30727
DPM1 223.39880 157.90301 117.785374 47.503563 121.970962 397.55616
SCYL3 61.48895 43.46170 33.390772 13.466703 15.764700 51.38398
C1orf112 48.08741 33.98920 9.168716 3.697799 16.426812 53.54209
X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6 3.32685727 47.513181 19.2650826 31.1332826 7.9194927 3.139009e+01
TNMD 0.03494839 4.223713 1.7125812 0.6216078 0.1581208 3.472172e-10
DPM1 11.89742238 44.383901 17.9962591 24.0922175 6.1284299 3.307912e+01
SCYL3 1.58380220 17.297378 7.0135364 9.6705329 2.4599306 1.078385e+01
C1orf112 0.57945053 2.281451 0.9250559 0.4478465 0.1139204 1.102016e+00
X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6 4.929200e+01 8.409561e+00 9.467003e+00 5.021394e+01 2.145622e+01 1.381350e+01
TNMD 5.452367e-10 2.089263e-11 2.351973e-11 1.443593e-09 6.168413e-10 8.919395e-11
DPM1 5.194429e+01 7.341338e+00 8.264458e+00 1.094567e+02 4.677043e+01 2.494379e+01
SCYL3 1.693392e+01 2.464982e+00 2.774936e+00 8.967997e+00 3.831989e+00 2.104914e+00
C1orf112 1.730500e+00 8.844547e-02 9.956686e-02 3.486952e+00 1.489960e+00 2.873641e-01
X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6 8.388777e+00 105.289845 11.6952038 39.0120451 15.2885771 50.410794
TNMD 5.416643e-11 4.441261 0.4933187 0.3695982 0.1448432 12.884750
DPM1 1.514807e+01 105.396217 11.7070192 32.3502584 12.6778645 80.801015
SCYL3 1.278289e+00 25.031901 2.7804503 7.9134411 3.1012282 20.121823
C1orf112 1.745128e-01 9.447006 1.0493382 1.0486089 0.4109433 3.840084
X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6 93.359429 60.254296 31.5137943 81.72363 17.847013 70.666160
TNMD 23.862209 3.459009 1.8091077 45.24704 9.881162 8.787499
DPM1 149.641299 80.005860 41.8441238 172.37450 37.643577 123.474518
SCYL3 37.265073 20.520650 10.7325717 47.01946 10.268229 34.689721
C1orf112 7.111732 1.375031 0.7191592 27.75975 6.062245 7.190955
X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6 71.174743 165.064544 15.144349 198.915006 57.877079 7.448451e+00
TNMD 8.850742 4.194117 0.384802 1.135182 0.330297 3.039280e-10
DPM1 124.363162 172.650299 15.840327 172.354087 50.148811 1.708884e+01
SCYL3 34.939383 60.056705 5.510085 61.749660 17.966920 1.006046e+01
C1orf112 7.242708 28.998964 2.660598 10.468956 3.046088 3.307160e-08
X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6 8.463970e+00 1.334683e+01 3.128566e+01 6.808912e+01 6.146158e+01 1.783278e+01
TNMD 3.453654e-10 1.223191e-10 3.694867e-10 8.041393e-10 1.630304e-10 4.221172e-10
DPM1 1.941872e+01 2.536677e+01 2.704933e+01 5.886930e+01 4.402054e+01 6.899054e+01
SCYL3 1.143210e+01 1.538116e+01 1.026548e+01 2.234147e+01 1.720668e+01 2.994818e+00
C1orf112 3.758057e-08 1.775312e-08 1.394713e+00 3.035410e+00 8.208248e-01 4.924430e-08
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6 1.877028e+01 6.098487e+00
TNMD 4.443086e-10 3.242257e-11
DPM1 7.261748e+01 1.954488e+01
SCYL3 3.152260e+00 8.738418e-01
C1orf112 5.183315e-08 5.045058e-09
25450 more rows ...
$deviance
[1] 64.18447 22.23679 26.23842 32.44059 29.32841
25450 more elements ...
$iter
[1] 8 22 6 7 18
25450 more elements ...
$failed
[1] FALSE FALSE FALSE FALSE FALSE
25450 more elements ...
$method
[1] "levenberg"
$counts
X102_tibia_non.sclerotic_pellet X102_tibia_sclerotic_adipocyte X102_tibia_sclerotic_pellet X104_tibia_non.sclerotic_adipocyte X104_tibia_non.sclerotic_pellet X105_tibia_non.sclerotic_adipocyte
TSPAN6 3 18 28 12 17 26
TNMD 0 0 0 0 1 10
DPM1 177 29 42 33 57 6
SCYL3 61 26 10 26 7 14
C1orf112 71 0 0 0 9 0
X105_tibia_sclerotic_adipocyte X109_tibia_non.sclerotic_adipocyte X109_tibia_sclerotic_adipocyte X109_tibia_sclerotic_pellet X128_tibia_non.sclerotic_adipocyte X128_tibia_non.sclerotic_pellet
TSPAN6 9 43 45 33 16 75
TNMD 3 4 0 0 0 0
DPM1 19 70 62 33 34 153
SCYL3 6 10 13 30 4 24
C1orf112 0 1 22 0 0 6
X128_tibia_sclerotic_adipocyte X128_tibia_sclerotic_pellet X130_Tibia_non.sclerotic_adipocyte X130_Tibia_non.sclerotic_pellet X130_Tibia_sclerotic_adipocyte X130_Tibia_sclerotic_pellet
TSPAN6 5 6 28 4 3 9
TNMD 0 0 0 0 0 0
DPM1 6 23 38 159 13 19
SCYL3 5 6 8 16 0 7
C1orf112 0 0 2 23 0 0
X144_Tibia_non.sclerotic_adipocyte X144_Tibia_non.sclerotic_pellet X144_Tibia_sclerotic_adipocyte X144_Tibia_sclerotic_pellet X148_Tibia_non.sclerotic_adipocyte X148_Tibia_non.sclerotic_pellet
TSPAN6 65 26 62 22 33 17
TNMD 1 0 0 7 3 0
DPM1 174 218 105 45 101 356
SCYL3 50 38 31 19 18 37
C1orf112 16 37 14 4 19 75
X148_Tibia_sclerotic_adipocyte X149_Tibia_non.sclerotic_adipocyte X149_Tibia_non.sclerotic_pellet X149_Tibia_sclerotic_adipocyte X149_Tibia_sclerotic_pellet X151_Tibia_non.sclerotic_adipocyte
TSPAN6 7 59 15 33 7 4
TNMD 0 13 0 0 0 0
DPM1 16 66 20 27 0 26
SCYL3 2 12 4 21 1 11
C1orf112 0 0 0 2 0 0
X151_Tibia_non.sclerotic_pellet X151_Tibia_sclerotic_adipocyte X151_Tibia_sclerotic_pellet X155_Tibia_non.sclerotic_adipocyte X155_Tibia_non.sclerotic_pellet X155_Tibia_sclerotic_adipocyte
TSPAN6 42 0 30 43 29 16
TNMD 0 0 0 0 0 0
DPM1 48 15 3 96 45 28
SCYL3 23 0 4 21 0 1
C1orf112 4 0 0 3 3 0
X155_Tibia_sclerotic_pellet X156_Tibia_non.sclerotic_adipocyte X156_Tibia_non.sclerotic_pellet X156_Tibia_sclerotic_adipocyte X156_Tibia_sclerotic_pellet X159_Tibia_non.sclerotic_adipocyte
TSPAN6 5 75 26 7 16 66
TNMD 0 12 0 0 0 8
DPM1 16 59 12 26 22 79
SCYL3 1 38 4 5 1 36
C1orf112 0 10 1 0 1 2
X159_Tibia_non.sclerotic_pellet X159_Tibia_sclerotic_adipocyte X159_Tibia_sclerotic_pellet X160_Tibia_non.sclerotic_adipocyte X160_Tibia_non.sclerotic_pellet X160_Tibia_sclerotic_adipocyte
TSPAN6 66 68 27 135 11 87
TNMD 5 11 0 12 0 33
DPM1 150 85 40 155 49 125
SCYL3 26 3 15 27 14 33
C1orf112 6 2 1 8 11 8
X160_Tibia_sclerotic_pellet X161_Tibia_non.sclerotic_adipocyte X161_Tibia_non.sclerotic_pellet X161_Tibia_sclerotic_adipocyte X161_Tibia_sclerotic_pellet X163_Tibia_non.sclerotic_adipocyte
TSPAN6 33 107 24 110 75 17
TNMD 0 13 0 0 0 0
DPM1 100 266 10 140 48 23
SCYL3 40 44 12 38 12 19
C1orf112 6 9 0 18 6 0
X163_Tibia_non.sclerotic_pellet X163_Tibia_sclerotic_adipocyte X164_tibia_non.sclerotic_adipocyte X164_tibia_non.sclerotic_pellet X164_tibia_sclerotic_pellet X99_Tibia_non.sclerotic_adipocyte
TSPAN6 3 6 52 65 25 4
TNMD 0 0 0 0 0 0
DPM1 25 10 32 54 40 25
SCYL3 4 12 11 16 21 0
C1orf112 0 0 1 6 0 0
X99_Tibia_non.sclerotic_pellet X99_Tibia_sclerotic_pellet
TSPAN6 31 7
TNMD 0 0
DPM1 84 30
SCYL3 6 1
C1orf112 0 0
25450 more rows ...
$unshrunk.coefficients
(Intercept) patientX104 patientX105 patientX109 patientX128 patientX130 patientX144 patientX148 patientX149 patientX151 patientX155 patientX156 patientX159 patientX160 patientX161 patientX163 patientX164
TSPAN6 -12.25755 0.04478320 0.84363162 0.60858193 0.16293812 0.1250750 0.06856748 -0.02670748 0.7560022 1.08254262 0.22274700 1.01586840 0.4501357 0.360303891 0.9217194 -0.1268412 1.0788126
TNMD -36.08000 20.45165457 24.16241695 21.29150717 -0.24967565 -0.3183288 22.96086067 20.73326559 22.1581629 -0.32256717 -0.22722357 21.67254299 22.9084281 23.591551124 21.0715188 -0.2266244 -0.2608003
DPM1 -11.15765 0.06879415 -0.62607410 -0.06332566 -0.09365573 0.2747873 0.11639440 0.33594356 -0.4120290 0.03505174 -0.09791717 -0.08302267 -0.1779809 0.006729252 -0.1332498 -0.3963228 -0.1665859
SCYL3 -11.98369 -0.03910725 0.04087282 -0.38980864 -0.68838362 -0.6042595 -0.34766866 -0.88402832 -0.5283130 -0.25976330 -1.77374632 -0.69456049 -0.7421276 -0.466340660 -0.3631909 -0.1000977 -0.3094233
C1orf112 -12.95906 -0.49407197 -18.47705653 0.80542184 -2.17192809 -0.6462131 0.38186723 0.13248649 -1.5786830 -1.56529866 -1.74300768 -0.69364055 -1.4230651 -0.017941884 -0.1158468 -18.6579279 -1.3301482
patientX99 groupsclerotic
TSPAN6 0.2301995 0.04397152
TNMD -0.4141237 -1.44945922
DPM1 0.4832296 -0.14428669
SCYL3 -1.8278183 -0.11477028
C1orf112 -18.7758008 -1.16141534
25450 more rows ...
$df.residual
[1] 43 43 43 43 43
25450 more elements ...
$design
(Intercept) patientX104 patientX105 patientX109 patientX128 patientX130 patientX144 patientX148 patientX149 patientX151 patientX155 patientX156 patientX159 patientX160 patientX161
X102_tibia_non.sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X102_tibia_sclerotic_adipocyte 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X102_tibia_sclerotic_pellet 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
X104_tibia_non.sclerotic_adipocyte 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
X104_tibia_non.sclerotic_pellet 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
patientX163 patientX164 patientX99 groupsclerotic
X102_tibia_non.sclerotic_pellet 0 0 0 0
X102_tibia_sclerotic_adipocyte 0 0 0 1
X102_tibia_sclerotic_pellet 0 0 0 1
X104_tibia_non.sclerotic_adipocyte 0 0 0 0
X104_tibia_non.sclerotic_pellet 0 0 0 0
57 more rows ...
$offset
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 16.2362 14.91478 14.9368 14.7865 14.96641 14.17901 14.51094 15.2927 15.30689 15.36794 14.63179 16.17223 13.89043 14.37602 15.09495 15.87542 13.82725 13.4649 16.45021 16.10324 15.95441 15.04635 15.62549 16.80704
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 13.44231 15.36255 14.45984 14.89585 13.5269 14.6215 15.07277 13.26041 13.37885 15.9511 15.10082 14.61648 14.11773 15.8984 13.70086 14.86158 13.92482 15.72762 16.34387 15.86202 15.21387 16.30059 14.77908 16.11124
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] 16.11841 16.44217 14.05346 16.58474 15.35018 14.3924 14.52021 14.9317 14.6219 15.39955 15.25318 14.90839 14.95963 13.79142
attr(,"class")
[1] "CompressedMatrix"
attr(,"Dims")
[1] 5 62
attr(,"repeat.row")
[1] TRUE
attr(,"repeat.col")
[1] FALSE
25450 more rows ...
$dispersion
[1] 0.4141750 3.8966115 0.3095450 0.7440241 2.1049333
25450 more elements ...
$prior.count
[1] 0.125
$AveLogCPM
[1] 3.1056355 -0.2543233 3.7623396 2.0162150 0.4687608
25450 more elements ...
$df.residual.zeros
[1] 43 23 43 43 38
25450 more elements ...
$df.prior
[1] 25.67789 25.67789 25.67789 25.67789 25.67789
25450 more elements ...
$var.post
[1] 1.3267538 0.8990513 0.7296690 0.9086660 0.8755580
25450 more elements ...
$var.prior
[1] 1.0489252 0.8383528 0.9297378 1.1669445 1.0291059
25450 more elements ...
$samples57 more rows ...
$genes25450 more rows ...
$tibia_sclerotic_vs_non_sclerotic$mds_plot
$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect
$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$w
[1] 1.633991
$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$h
[1] 0.7924232
$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$left
[1] 2.503014
$tibia_sclerotic_vs_non_sclerotic$mds_plot$rect$top
[1] 2.270144
$tibia_sclerotic_vs_non_sclerotic$mds_plot$text
$tibia_sclerotic_vs_non_sclerotic$mds_plot$text$x
[1] 2.842382 2.842382
$tibia_sclerotic_vs_non_sclerotic$mds_plot$text$y
[1] 2.006003 1.741862
$tibia_sclerotic_vs_non_sclerotic$ql_disp_plot
NULL
$tibia_sclerotic_vs_non_sclerotic$boxplot_gg
$volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic
$volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic
$volcano_hip_adipocytes_sclerotic_vs_non_sclerotic
$volcano_hip_pellet_sclerotic_vs_non_sclerotic
$volcano_hip_sclerotic_vs_non_sclerotic
$volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
$volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic
$volcano_tibia_pellet_sclerotic_vs_non_sclerotic
$volcano_tibia_sclerotic_vs_non_sclerotic
volcano
plot_volcano <- function(results_table,
gene_column = "genes",
logFC_column = "logFC",
FDR_column = "FDR",
genes_of_interest = NULL,
#output_file = paste0("volcano_plot.",format_plot),
output_file = NULL,
format_plot = "tiff",
up_color = "#d00000",
down_color = "#3f88c5",
ns_color = "#f2e9e4",
up_size = 2,
down_size = 2,
ns_size = 1,
up_alpha = 1,
down_alpha = 1,
ns_alpha = 0.5,
x_limits = c(-10, 10),
y_threshold = -log10(0.05),
x_label = "Log2 Fold Change",
y_label = "-Log10 Adjusted P-Value") {
# Mutate the gene type
results_table <- results_table |>
dplyr::mutate(gene_type = dplyr::case_when(
!!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
!!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
TRUE ~ "Not selected"
)) |>
dplyr::filter(!!rlang::sym(gene_column) != "")
# Get the top up and down genes
ints_up <- results_table |>
dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) > 1) |>
dplyr::arrange(!!rlang::sym(FDR_column)) |>
dplyr::slice(1:10) |>
dplyr::pull(!!rlang::sym(gene_column))
ints_down <- results_table |>
dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) < -1) |>
dplyr::arrange(!!rlang::sym(FDR_column)) |>
dplyr::slice(1:10) |>
dplyr::pull(!!rlang::sym(gene_column))
ints <- c(ints_up, ints_down)
ints_genes <- results_table |>
dplyr::filter(!!rlang::sym(gene_column) %in% ints) |>
dplyr::distinct(!!rlang::sym(gene_column), .keep_all = TRUE)
if (!is.null(genes_of_interest)) {
to_add_genes <- results_table |>
dplyr::filter(!!rlang::sym(gene_column) %in% genes_of_interest) |>
dplyr::mutate(gene_type = dplyr::case_when(
!!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
!!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
TRUE ~ "Not Selected"))
results_table <- rbind(results_table, to_add_genes)
ints_genes <- rbind(ints_genes, to_add_genes)
}
# Define the plot
p <- results_table |>
ggplot(aes(x = !!rlang::sym(logFC_column),
y = -log10(!!rlang::sym(FDR_column)))) +
geom_point(aes(colour = gene_type),
alpha = 0.8,
shape = 16,
size = 1) +
geom_hline(yintercept = y_threshold,
linetype = "dashed") +
geom_vline(xintercept = c(log2(0.5), log2(2)),
linetype = "dashed") +
geom_point(data = dplyr::filter(ints_genes, gene_type == "up"),
shape = 21,
size = 2,
fill = "tomato3",
colour = "black") +
geom_point(data = dplyr::filter(ints_genes, gene_type == "down"),
shape = 21,
size = 2,
fill = "steelblue",
colour = "black") +
geom_label_repel(data = ints_genes, # Add labels last to appear as the top layer
aes(label = !!rlang::sym(gene_column)),
force = 2,
nudge_y = .2, nudge_x = 0.1,
max.overlaps = 30, size = 2) +
scale_color_manual(values = c("Upregulated" = up_color,
"Downregulated" = down_color,
"Not Selected" = ns_color)) +
scale_x_continuous(breaks = c(seq(-10, 10, 2)),
limits = x_limits) +
labs(x = x_label, y = y_label, color = "Genes") +#title = title
#theme_void() + # Remove background
#theme(legend.position = "none") # Remove legend if not needed
theme_classic(base_size = 14) +
theme(
plot.title = element_text(hjust = 0.5, face = "bold"),
legend.position = "right",
legend.title = element_text(size = 12),
legend.text = element_text(size = 10)
)
if (!is.null(genes_of_interest)) {
p <- p + geom_point(data = to_add_genes,
shape = 21,
size = 2.4,
fill = "#70e000",
colour = "black")
}
# Save the plot
if (!is.null(output_file)) {
ggsave(plot = p,
filename = output_file,
device = format_plot,
dpi = 300,
units = "in",
width = 7, height = 12)
}
return(p)
}
HERE IF WANNA SAVE THE PLOT CHANGE THE OUTPUT FILE
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[1]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic
#pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
comparison_names[8][1] "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic"#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[8]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
Hips
comparison_names[5][1] "hip_adipocytes_sclerotic_vs_non_sclerotic"#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[5]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic
comparison_names[6][1] "hip_pellet_sclerotic_vs_non_sclerotic"volcano_hip_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[6]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_pellet_sclerotic_vs_non_sclerotic
comparison_names[7][1] "hip_sclerotic_vs_non_sclerotic"volcano_hip_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[7]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_sclerotic_vs_non_sclerotic
Tibias
comparison_names[9][1] "tibia_adipocytes_sclerotic_vs_non_sclerotic"volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[9]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic
comparison_names[10][1] "tibia_pellet_sclerotic_vs_non_sclerotic"volcano_tibia_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[10]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_pellet_sclerotic_vs_non_sclerotic
comparison_names[11][1] "tibia_sclerotic_vs_non_sclerotic"volcano_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[11]]]$results$table,
#format_plot="tiff",
#output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_sclerotic_vs_non_sclerotic
comparison_names
[1] "adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic" "bone_hip_vs_tibia" "bone_non_sclerotic_hip_vs_tibia"
[4] "bone_sclerotic_hip_vs_tibia" "hip_adipocytes_sclerotic_vs_non_sclerotic" "hip_pellet_sclerotic_vs_non_sclerotic"
[7] "hip_sclerotic_vs_non_sclerotic" "pellets_hip_and_tibia_sclerotic_vs_non_sclerotic" "tibia_adipocytes_sclerotic_vs_non_sclerotic"
[10] "tibia_pellet_sclerotic_vs_non_sclerotic" "tibia_sclerotic_vs_non_sclerotic" "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non_sclerotic"
[13] "volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic" "volcano_hip_adipocytes_sclerotic_vs_non_sclerotic" "volcano_hip_pellet_sclerotic_vs_non_sclerotic"
[16] "volcano_hip_sclerotic_vs_non_sclerotic" "volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic" "volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic"
[19] "volcano_tibia_pellet_sclerotic_vs_non_sclerotic" "volcano_tibia_sclerotic_vs_non_sclerotic" ---
title: "Volcanos"
output: html_notebook
---

Before running this script, you need to run all the analysis first so the variable are available.

# run volcanos for all the comparisons of interest
```{r}

```


# Get comparisons 
```{r}
ls(all.names = TRUE)
# Get all object names that match a pattern
comparison_names <- ls(pattern = "vs")
comparison_names
```


```{r}
comparisons_list <- mget(comparison_names)
comparisons_list

```


# volcano
```{r}
plot_volcano <- function(results_table, 
                         gene_column = "genes", 
                         logFC_column = "logFC", 
                         FDR_column = "FDR", 
                         genes_of_interest = NULL, 
                         #output_file = paste0("volcano_plot.",format_plot),
                         output_file = NULL,
                         format_plot = "tiff",
                         up_color = "#d00000", 
                         down_color = "#3f88c5", 
                         ns_color = "#f2e9e4", 
                         up_size = 2, 
                         down_size = 2, 
                         ns_size = 1,
                         up_alpha = 1, 
                         down_alpha = 1, 
                         ns_alpha = 0.5,
                         x_limits = c(-10, 10),
                         y_threshold = -log10(0.05),
                         x_label = "Log2 Fold Change",
                         y_label = "-Log10 Adjusted P-Value") {
  
  # Mutate the gene type
  results_table <- results_table |>
    dplyr::mutate(gene_type = dplyr::case_when(
      !!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
      !!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
      TRUE ~ "Not selected"
    )) |>
    dplyr::filter(!!rlang::sym(gene_column) != "")
  
  # Get the top up and down genes
  ints_up <- results_table |>
    dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) > 1) |>
    dplyr::arrange(!!rlang::sym(FDR_column)) |>
    dplyr::slice(1:10) |>
    dplyr::pull(!!rlang::sym(gene_column))
  
  ints_down <- results_table |>
    dplyr::filter(!!rlang::sym(FDR_column) < 0.05 & !!rlang::sym(logFC_column) < -1) |>
    dplyr::arrange(!!rlang::sym(FDR_column)) |>
    dplyr::slice(1:10) |>
    dplyr::pull(!!rlang::sym(gene_column))
  
  ints <- c(ints_up, ints_down)
  
  ints_genes <- results_table |>
    dplyr::filter(!!rlang::sym(gene_column) %in% ints) |>
    dplyr::distinct(!!rlang::sym(gene_column), .keep_all = TRUE)
  
  if (!is.null(genes_of_interest)) {
    to_add_genes <- results_table |>
      dplyr::filter(!!rlang::sym(gene_column) %in% genes_of_interest) |> 
      dplyr::mutate(gene_type = dplyr::case_when(
        !!rlang::sym(logFC_column) > 1 & !!rlang::sym(FDR_column) < 0.05 ~ "Upregulated",
        !!rlang::sym(logFC_column) < -1 & !!rlang::sym(FDR_column) < 0.05 ~ "Downregulated",
        TRUE ~ "Not Selected"))
    results_table <- rbind(results_table, to_add_genes)
    ints_genes <- rbind(ints_genes, to_add_genes)
  }
  
  # Define the plot
  p <- results_table |>
    ggplot(aes(x = !!rlang::sym(logFC_column),
               y = -log10(!!rlang::sym(FDR_column)))) +
    geom_point(aes(colour = gene_type), 
               alpha = 0.8, 
               shape = 16,
               size = 1) +
    geom_hline(yintercept = y_threshold,
               linetype = "dashed") + 
    geom_vline(xintercept = c(log2(0.5), log2(2)),
               linetype = "dashed") +
    geom_point(data = dplyr::filter(ints_genes, gene_type == "up"),
               shape = 21,
               size = 2,
               fill = "tomato3", 
               colour = "black") + 
    geom_point(data = dplyr::filter(ints_genes, gene_type == "down"),
               shape = 21,
               size = 2,
               fill = "steelblue", 
               colour = "black") +
    geom_label_repel(data = ints_genes, # Add labels last to appear as the top layer  
                     aes(label = !!rlang::sym(gene_column)),
                     force = 2,
                     nudge_y = .2, nudge_x = 0.1,
                     max.overlaps = 30, size = 2) +
    scale_color_manual(values = c("Upregulated" = up_color,
                                  "Downregulated" = down_color,
                                  "Not Selected" = ns_color)) +
    scale_x_continuous(breaks = c(seq(-10, 10, 2)),     
                       limits = x_limits) +
    labs(x = x_label, y = y_label, color = "Genes") +#title = title

    #theme_void() +  # Remove background
    #theme(legend.position = "none")  # Remove legend if not needed
    theme_classic(base_size = 14) +
    theme(
    plot.title = element_text(hjust = 0.5, face = "bold"),
    legend.position = "right",
    legend.title = element_text(size = 12),
    legend.text = element_text(size = 10)
  )
  
  if (!is.null(genes_of_interest)) {
    p <- p + geom_point(data = to_add_genes,
                        shape = 21,
                        size = 2.4,
                        fill = "#70e000", 
                        colour = "black")
    }
  # Save the plot
  if (!is.null(output_file)) {
    ggsave(plot = p,
           filename = output_file,
           device = format_plot,
           dpi = 300,
           units = "in",
           width = 7, height = 12)
  }
  
  return(p)
}

```


## HERE IF WANNA SAVE THE PLOT CHANGE THE OUTPUT FILE

```{r}
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[1]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_adipocyte_hip_and_tibia_sclerotic_vs_non.sclerotic

```

```{r}
#pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
comparison_names[8]
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[8]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_pellets_hip_and_tibia_sclerotic_vs_non_sclerotic
```

# Hips
```{r}
comparison_names[5]
#path_volc = "~/CLUSTER/Environments/2024_07_05_Lea_Lausanne_Hip_Tibia_BRBseq/Analysis_removed_samples/DGE_Results_tables/adipocytes_patient/"
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[5]]]$results$table,
                                                                           #format_plot="tiff",
                                                                           #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                                           gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_adipocytes_sclerotic_vs_non_sclerotic
```
```{r}
comparison_names[6]
volcano_hip_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[6]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_pellet_sclerotic_vs_non_sclerotic
```


```{r}
comparison_names[7]
volcano_hip_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[7]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_hip_sclerotic_vs_non_sclerotic
```
# Tibias
```{r}
comparison_names[9]
volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[9]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_adipocytes_sclerotic_vs_non_sclerotic
```
```{r}
comparison_names[10]
volcano_tibia_pellet_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[10]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_pellet_sclerotic_vs_non_sclerotic
```
```{r}
comparison_names[11]
volcano_tibia_sclerotic_vs_non_sclerotic <- plot_volcano(results_table = comparisons_list[[comparison_names[11]]]$results$table,
                                                              #format_plot="tiff",
                                                              #output_file = paste0(path_volc,"volcano_",comparison_names[1],".tiff"),
                                                              gene_column = "genes",genes_of_interest = c("IL11","RCN2", "IL11", "CNTNAP2", "STMN2"))
volcano_tibia_sclerotic_vs_non_sclerotic
```

```{r}
comparison_names
```

